Says It All

Thank you Why Evolution Is True for this little gem:

Non C'è Due Senza Tre...

I'd like to close this boss trifecta with a common Italian saying, literally translated as there is no two without three, and a big thanks to Why Evolution Is True for posting this video of Bill Nye the Science Guy. I adored Bill Nye as a kid, along with Kratts Creatures he was my main source of science growing up, ironically educating me even more in many areas than my science teachers in elementary and middle school. 

Sometimes, you find out that the people on TV that you loved as a kid turn out to be not so great in real life (I almost cried when I heard about the racial slurs thrown out there by Kramer, or how Frasier is actually a right-wing nut) but not this time! Bill Nye turns out to be just as cool in real life as he was on TV, as illustrated by his willingness and sincerity in coming out publicly against creationism.

Coincidence that three days later a rumor on twitter spread that he was dead? Probably not, but who cares. Bill Nye, you rock.

How About A Litte Good Science?

Homosexuality and it's evolution has been a topic that has intrigued me ever since I attended a lecture on the subject during my third year in college. It is a dynamic and fascinating field and one that is too often oversimplified and overlooked, especially by those who refuse to accept it. I think that potholder54 did a very good job summarizing people's issues with it and the science behind it, and I wanted to share it here.

I have that book that Ricky Gervais is talking about, and it is very good. However, for a book that is more about the evolutionary theory (rather than a huge collection of examples) an excellent book is Evolution's Rainbow: Diversity, Gender and Sexuality in Nature and People by Joan Roughgarden. I don't 100% agree with absolutely everything she says, but it does bring a great perspective on a topic that is far more complex than we ever could have imagined.

Ooh! A (Very, Very Long) Response...

So remember that post I wrote answering a creationist’s questions about abiogenesis? I got three PMs in response, which was actually quite surprising since they usually spam me with copy and pasted questions and then scamper off when I respond. However, as I said I will answer any question that is asked of me to the best of my abilities, regardless of whether or not I think they won’t reply, and in this case he did. Well, let’s take a look shall we?

Well, I got the answer I get from virtually every atheist or evolutionist I encounter. They say evolution has nothing to do with abiogenesis and that you can believe in evolution without having to worry about deciding where life came from. There is a huge problem here. First of all, you are overlooking the obvious fact that evolution is directly linked with abiogenesis. If there is no life, we cannot evolve from anything. If life cannot come from nonliving material, evolution is not possible. If there is no God, obviously life HAD to come into existence by itself andit HAD to be from nonliving material. Your argument that evolution has nothing to do with abiogenesis is simply incorrect.

All of the fields of biology and even science are linked in some way, that does not mean that evidence for (or lack thereof) of one discipline means that the other is false. By the same rationale you could say well the theory of evolution is directly linked with the theory of gravity, because without gravity all life would fall off the planet and float around in space, so any problems found with the theory of gravity mean evolution is a lie! Modern medicine is directly linked with evolution because without evolution there would be no vaccine development or reason to test drugs on animals, I don’t believe in evolution therefore I won’t go to the doctor! Just because the fields of science are interconnected does not mean that the evidence for them is in the way you are suggesting.

Now, onto your next attempt at answering my questions. You gave me details about a peptide being created and attempted to pass that off as life. I truly hope you were joking or maybe you were not thinking clearly because this is the most ridiculous answer I have ever gotten.If you want a more specific definition of life, how about this? A single-celled organism. Tell me where a single-celled organism has arisen in a lab from nonliving material. THAT is life. Do not give me the details about a peptide being created. That is completely ridiculous.

I am not trying to “pass” anything off as anything, I was giving an example of something that could conceivably represent a step between non-living and life, while illustrating that defining life is very difficult. Don’t the pro-lifers constantly say that IVF technicians are “creating life” every time they combine sperm and egg?

 So your definition of life is something that has a cell wall? Ham Smith and Clyde Hutchinson made a self-replicating bacteria in May 2010 at the J. Craig Venter Institute in San Diego, by chemically making its genome in the lab after having designed it in a computer. My guess is that is not going to be enough either, and you’ll change the definition of life again. The point I still don’t understand is why you are so hung up on scientists creating life as the ultimate proof of abiogenesis. Even if scientists created a frog in the lab from scratch, one that is in every way indistinguishable from a frog born from frogspawn, what would that matter? That would be nothing more than a pointless, extremely expensive endeavour, not proving or providing any evidence for abiogenesis. Ironically, the example of the self-replicating peptide is far more interesting in the scope of abiogenesis than making an animal in a lab is, but you dismiss it as “ridiculous”, which leads me to believe you actually don’t read up much on the evidence for abiogenesis as you previously claimed.

A peptide is a molecule consisting of 2 or more amino acids. Peptides are smaller than proteins, which are also chains of amino acids. Molecules small enough to be synthesized from the constituent amino acids are, by convention, called peptides rather than proteins. The dividing line is at about 50 amino acids. Depending on the number of amino acids, peptides are called dipeptides, tripeptides, tetrapeptides, and so on. These are some of the components that make up living organisms, however they are not living organisms themselves. Many experiments have been conducted attempting to create life from nonliving material using these "ingredients of life". However, they have all failed. They have even used conditions that are unrealistic in the natural world in an attmept to create living organsims. In more simplistic terminology, they were cheating in an attempt to create any sort of living organism. Sadly, even though they were using unrealistic conditions that were in their favor, they stil cannot create life.

Could you please provide your sources? What poor scientists were desperately trying to create life in an attempt to provide evidence for abiogenesis?

 I am feeling generous today, I will give you another chance to answer my question. Also, you say since scientists cannot create life, it is unreasonable to automatically assume "God did it". I am not saying it automatically proves that God did it. What I am saying is that the fact that we cannot create life is CONSISTENT with biblical scripture. It is NOT CONSISTENT with evolutionary/abiogenesis teaching. If life arose from nonliving material completely by chance, we should be able to replicate that process. However, we cannot. If God made life, we should not able to replicate that process. And guess what? We cannot create life.

Might I point out that a scientist actively creating something alive in the lab is not life “arising by chance” and therefore would still not provide the evidence that you are so desperately looking for?

And how is this consistent with biblical scripture? Does the bible say that humans will not be able to create life? And even if it did, what about all of the things that are in scripture like classifying bats as birds  or a man being able to live to see his 800^th birthday, which are completely inconsistent with reality? What do those parts of the bible say to its veracity and unerring nature?

Also, in response to your attempt at answering my quetion, you gave me a false answer about the peptide being created in 1996.
Here is a quote from the website detailing your findings:

(It wouldn't let my copy and paste, but feel free to google this statement. I copied it word for word from the article detailing the 1996 experiment you discussed.)

"Because the peptide with 32 amino acids facilitates the formation of this single peptide bond, Lee claims that this peptide can self-replicate. But is this really true? To self-replicate, this peptide requires a pool of two peptides. One of these peptides has the same amino acid sequence as the first 15 amino acids in the self-replicating peptide, and the other has the amino acid sequence as the next 17 amino acids. Where do these peptides come from? In this case, they are supplied by the investigator."

Did you forget to mention that part? I think you did. Wow- scientists cannot even create self-replicating peptides from nonliving material. That is pretty sad. 

I did google it and guess what? It comes from a creationist website (of course). Not including what a creationist had to say is not forgetting, it’s omitting irrelevant information. However the fact that a creationist found Lee et al’s work to be important enough to try to butcher on their website should be an indication that it is not as “ridiculous” work as you think. If you want the real information the paper is free, which is one of the reasons I picked it, you can find it and read it yourself here 

As for you saying no scientist would say that E.Coli or anything similar to that would suddenly pop out of the ground, I completely agree with you. However, the bottom line is that there are NO examples of life coming from nonliving material in nature (The Law of Biogenesis) and we cannot create life from nonliving material in a lab.

The Law of Biogenesis, as in Pasteur circa 1860? I agree with him that spontaneous generation is not correct, but we really have come quite a way in science in the past century and a half. 

After 24 hours, I got this amusing little follow-up

You completely ignored my statements. You refused to admit that I proved scientists could not create the peptide you claimed and that your attempts at debating me have failed in every respect. You refuse to see the evidence and stubbornly hold on to nothing to support your ridiculous claims. You didn't reply to any of my arguments. You are truly pathetic.

Honey, when you have two jobs, deadlines coming up, squeezing in travel time and being a part-time youtuber and blogger, not getting back to you within a day is not called “ignoring [your] statements”, it’s called “being busy” (or “having a life”, if I want to be snarky about it).

So since you obviously have far more time on your hands than I do, why don’t you state your position a little more clearly (as well as providing the sources I asked for earlier):

1     1. What properties exactly does a bacteria possess that a self-replicating peptide does not that qualifies it as life?

         2. Why do you think creating a single-celled organism from scratch in a lab would disprove creationism and prove abiogenesis?

3  3.  How do you explain scripture that is blatantly inconsistent with reality? If your answer is “those parts are not literal”, then how do you objectively discriminate between what parts to take literally and which parts not to? If your answer is “back then those things were true/worked, they just aren’t/can’t now” then what evidence do you have of that? Has anyone been able to reproduce those ancient conditions in a lab and confirm what the bible says? (If not, by your logic, there’s a problem…)

And finally, and most importantly

        4. If you were to encounter the scientific experiment you seek, that fit all of your criteria unequivocally, would you begin to doubt creationism?

Think about that last one, because if the answer is no, there is absolutely no point in continuing to educate yourself in science or pestering scientists with questions you don’t want the answers to.

Unless you particularly enjoy building straw men and then beating them to death.


***EDITED TO ADD: I got a response back again from this guy. Apparently, pointing out that he's hanging his hat on a straw man is actually "admitting that [I'm] losing the debate". He didn't answer the questions, a part from saying that he would doubt creationism only if scientists created multi-cellular organisms every day in the lab (*facepalm*), did not address the fact that bacteria have been made repeatedly, and declared the "debate" over. As per my rule he has not responded with any new or relevant points, facts or opinions, so there goes another on the growing pile.

What Do You Mean By "Life"?

As an outspoken atheist and science-freak I often get asked some pretty standard questions about the more shall we say “controversial topics” in science. Some of them I cannot answer, some only in part, but many are so often repeated that I have decided to make blogposts out of the ones where I wind up having to repeat myself. This morning I got one such PM about abiogenesis, and since it is a pretty standard version of the questions I get about this topic I figured I’d post it here with my reply – a handy link to this post will save me time in the future.

Subject: Evolution

Well here we have our first problem. As I’m sure many of you have already heard, evolution is not a theory about the origins of life. Evolution explains the diversity of life as we see it today; it makes no speculation about how the very first living organism began. This may seem like splitting hairs for some, but it is fundamentally important.

You can believe in the theory of evolution without believing in the theory of abiogenesis, and I know far more people that choose this as their belief system than I know people who deny both. You can believe that the lighting that struck the primordial soup was God’s finger to zap together those first little building blocks of life, without denying a single piece of evidence that supports the theory of evolution. Even if scientists find a way to create a multicellular organism from nonliving compounds in a lab you can still believe that that’s not what actually happened all those billions of years ago. I’m not saying I agree or that it is particularly logical, but alas to each their own opinion.

I have a question for you. You obviously do not believe in God so I was wondering if you could help me out with something I have been wondering. Since life had to begin by chance from nonliving material I would like you to give me a SPECIFIC EXAMPLE of a living organism created ENTIRELY FROM NONLIVING MATERIAL in a lab, controlled environment, etc. ( I assume you know the difference between creating life from nonliving material and genetic engineering/bioengineering since genetic engineering and bioengineering are processes that deal with naturally occurring cells found in nature as well as DNA. Obviously this is not creating life from nonliving material.)

Well here we have another problem. What does God have to do with any of this? It is a common misconception that science exists to prove or disprove God, or that science has anything to do with the supernatural. If God is supernatural then by definition he (She? It.) lives outside of the natural world, and therefore cannot be tested for by natural means. Science involved testing the natural world, the two cannot be further apart.

Secondly, I do not like the “God of the gaps” fallacy that this question is implying. The argument “you can’t explain that! Therefore God” has no basis in logic or reasoning and you should all know this. It is a giant cop-out, and an arrogant way of implying that we as a species have learned everything that there is to know. The real statement to make about such things is “you can’t explain that yet”. Where would we be as a species if we were content with just “Goddidit” or “Devildidit”? Modern medicine, among other things would not exist.

I also spot a little misinterpretation of abiogenesis theory with “life had to begin by chance”, but he does not elaborate on the faux creationist probability argument so I’ll let it go as a slip up for now.

On to the question at hand. He wants a specific example of a living organism created by scientists, I’ll let him elaborate (and since genetic engineering is pretty much what I do yes, I know the difference between creating life and altering it).

Several examples of scientists who work with synthetic engineering and bioengineering are Dr. Venter and Dr. Szostak and multiple others.

They have admitted what they are doing is not creating life from nonliving material. The process of life coming from nonliving material is called abiogenesis so I want you give me a specific example of abiogenesis that has been successfully done in a lab by scientists. Since according to atheists life came into existence completely by chance billions of years ago, surely we can create life from nonliving material as well. So here is what I want you to give me IN SPECIFIC DETAIL:

1. The name of the organism that was created by scientists.
2. The location of the lab it was created in.
3. The name of the scientists who created it completely from nonliving material.
4. The year in which life was created by these scientists.

Well here we have to fix the goalpost from shifting with a simple question: What exactly do you mean by life? No scientist will tell you that a complex cellular organism popped up from nonliving materials in a single step: only creationists believe that complex organisms rose from nonliving material (In Genesis God makes Adam from clay, does he not?). Complex organisms came about after billions of years of evolution involving multiple steps that can be traced back to eventually a nonliving material. So at what point to we say this step is still nonliving, whereas the step right after can be called alive? It is a question that even scientists vehemently fight over. However, there are three criteria that are essential to calling something “alive”:

1. It has to be able to make copies of itself, either directly or by placing itself in such a way so as to take advantage of something else’s replicating machinery
2. Those copies have to resemble the original, meaning that the peculiarities of the original have to be “inherited” by its copies (although the copies need not be perfect)
3. Those copies also have to be able to replicate, as per criteria 1.

Those are the criteria that are indisputable, and whether or not to tack on more is something fought over. If you wish to bring up other criteria to tack on there we can certainly have a follow up of this debate.

Anyway, what evidence do we have of this so far? Well, a specific example could be the self-replicating peptide created in 1996. So let’s give him what he asked for:

1. Name: alpha-helical peptide based on the leucine-zipper domain of GCN4
2. Location: La Scripps Institute, La Jolla, California.
3. Scientists: David H. Lee, Juan R. Granja, Jose A. Martinez, Kay Severin, M. Reza Ghadiri.
4. Year: 1996

I’m guessing a self-replicating peptide is not going to be good enough for this person. However, before firing back with “a molecule is not alive! Give me LIFE!” please include a very clear definition of what you consider “life” to be. Also, please note that no scientist claims a fully functioning E. coli just popped out of the mud.

If you cannot answer these questions, there is a huge problem we have here. If life cannot come from nonliving material, there would be no life on the planet. So hopefully, you can give me these answers in very specific detail otherwise the idea that life can come from nonliving material is in serious trouble.

Again with this fallacy. Just because something has not been done in a lab does not mean that it cannot be explained. You cannot hold a star in your lab and watch it die, but astrophysicists can tell you what happens when one does. Even if you can’t do it in a lab because you don’t have an explanation does not mean that an explanation does not exist or is impossible. New things are discovered all the time, it is one of the wonders of humanity. 

Also, do not bother giving me THEORIES as to how life could have arrived here. I love reading those, I have read many of those, but I am looking for actual experimental results. I am not interested in theories that have never been proven. So, please, do yourself a favor and give me specific details about actual experimental results, not theories, because if you give me theories about how life could have come into existence on Earth by itself billions of years ago by chance from nonliving material, surely we can create life from nonliving material as well. Remember, no theories, just RESULTS. Thank you.

Well good, that saves me the time of looking up all of the evidence that there is in support of abiogenesis theory and reviewing it in bitesize chunks for this blog. For those of you who are not well versed in the evidence out there I strongly suggest searching for abiogenesis on the Talk Origins Website, they are much better at explaining it in a user-friendly way than I will ever be (especially since abiogenesis is very far from my field of expertise).

I hope this answers some questions for others as well, and I will always try to answer your questions to the best of my capabilities, so don’t hesitate to voice any concerns (but do hesitate on the trolling, for that I don’t have time).

Sources: Lee et. al (1996) A self-replicating peptide Nature: 328 525-528

Round Two: I Found The Copy Paste Site

So I'm tired, a little sick, have a half hour to kill, so what should I talk about today? Ooh I know, let me take a crack at another one of those silly creationist articles that Mogley52 so kindly spammed my creationism video with. This one is called THE SCIENCE SUPPORTING CREATION! Ooh, should be good, and why not? It has an oxymoron right there in the title. Turns out, I have found the source from which this particularly annoying creationist has copy and pasted his spamming comments from.

The first paragraph is enough to make a buzzer go off in my head every half a sentence. Mogley, you don't get to redefine the second law of thermodynamics to include "even in an open system". When you make a statement like that you have to show some reasoned scientific evidence to support what is now only your crackpot idea. No Mogley, Stephen Hawking is not an "evolutionary scientist". And why does God not need a beginning exactly, if you claim that everything, even time, must have one? Ugh we're going to have a seperate post about cosmology aren't we? Fine, but let's move on, I'm still waiting for some actual science that supports creation, just as soon as I wake up after knocking myself out from that facepalm.

OK I'm back. The next two paragraphs blather on about thermodynamics (which this guy has taken the liberty of redefining without giving any explanation as to how he got to these conclusions) and how Einstein believed in an Intelligent Creator (which is a hideous argument from authority which we have already established is complete bullshit regardless) so let's get to the good stuff in paragraph 4:

BIG BANG FLAWS: Big Bang scientists extrapolate a hypothetical scenario from a few facts. Yes, some galaxies are expanding, moving further away, but this is not the case with the entire universe. There are galaxies in the universe running perpendicular to the rest of the galaxies. That's contrary to Big Bang. If Big Bang really occurred, there should be a uniform distribution of gasses. 

WHAT?! Now I'm no physicist, by any stretch of the imagination, but I can see from a mile that this is total bullshit. Why the hell do we have to have uniform distribution of gases (and yes, I do know how to spell gases)?! Have you ever heard of, I dunno, gravity? The whole bit about how stars are born? Do me a favor, look it up, there is absolutely nothing incompatable between the big bang and the existence of gravity (trust me, they've notcied gravity exists already).


But from here we jump straight into evolution, so let's have at it!

Only evolution within biological "kinds" is genetically possible (i.e. varieties of dogs, cats, etc.), but not evolution across biological "kinds" (i.e. from worm to human). How did species survive if their vital tissues, organs, reproductive systems, etc. were still evolving?

You do realize that the idea that biological life is divided into "kinds" is one invented by creationists right? Notice how he stays away from the word "species", as speciation has also been demonstrated numerous times in the lab as well as observed in nature.


Creationists like this guy are fixated on the good old-fashioned Great Chain Of Being, as if evolution was this process with the ultimate goal in human perfection. Sorry to break it to you Mogley, that's an extremely self-centered view that is not remotely indicative of how things actually work. No, worms do not work their way up the chain of being to evolve into humans, that is ridiculous. Worms are very well adapted being just what they are, we are not the envy of the entire animal kingdom.

Animals have evloved as best they could with what they had to work with to fit in to the niche that they occupy. It is because of this that there are constraints on evolution, and there are certain features of certain animals that are not what any intelligent being would design. Why the hell do koalas have upside-down pouches, so that their babies' heads poke downwards? That looks dangerous right? Why on earth do blind cavefish still have rudimentary, yet completely non-functional eyes? Why do whales have completely useless leg bone stubs attached to their pelvis? None of these things would make sense if we are to believe that all creatures were perfectly, intelligently designed.

Look, this is getting really old, really fast. All of his articles are 70% linking to other articles, so none of them actually get into any meat of any sort of argument stating any sort of fact. He likes to just say things with no backup, like

The actual similarity is between 70-87% not 99.8% as commonly believed. The original research stating 99.8% similarity was based on ignoring contradicting evidence

Really? You set up your own Human and Chimp Genome Sequencing Project? Great! Let's see your work!

Nowhere in these articles is there a modicum of argument, let alone a rational one. Every article so far can be summed up as this:

1. I have evidence, these laws of physics I just made up say so!
2. EINSTEIN WAS SUPER SMART AND HE BELIEVED ME SO THERE
3. Read all my other articles where I actually talk about these things in more detail! No really, I just need the page hits
4. There is evidence that evolutionists make stuff up! Trust me, there is, some other creationist dude on the internet said so. Faith remember? Have faith that I found out the errors in the science, no need for me to actually tell you how I found them.
4. I am so smart those fancy pants evolutionists wont even talk to me

I've had enough. I want some real answers from you Mogley. Are other "evolutionists" too chickenshit to talk to you? You've "successfully answered" many before? OK, riddle me this:


What makes you think that the big bang is incompatible with the theory of gravity?

Show your work demonstrating that the second law of thermodynamics also applies to an open system

How do you explain the presence of terrible design flaws in animals, like the vas deferens looping around the ureter, the upside down koala pouch or the leg bones in whales?

Why would there need to be "microevolution within kinds" if everything was designed perfectly by an all-knowing, totally awesome intelligent creator? If creation was perfect, why does it need to adjust?

Please explain, in a nutshell, the theory of evolution, so that I can at least assertain that you actually understand the theory that you claim you do not believe in.


I eagerly await your detailed, scientific answers. No copy and pasting allowed.

Everybody Loves A Fake War

Be it a war on terror, a war on Xmas, a war on videogames, many people, Americans especially, seem to love them a fake war. So when I had my creationism video spammed by a creationsit yet again I was not surprised to see that one of the many creationist articles Mogley52 asked me to read was one entitled WAR AMONG EVOLUTIONISTS! 

I think I know where this is going, but let’s go ahead and take a look shall we? This might be fun!

Slight disclaimer: although this “article” mostly deals with evolution, it also contains digression into abiogenesis, cosmology and the like. I will have another post for other topics, but for the sake of clarity I will be focusing on this guy’s gripe with the mechanisms of evolution.

There is a war among evolutionists. Most evolutionists are Neo-Darwinian, believing in gradual change from one form of life to another, but a good growing minority of evolutionists believe in Punctuated Equilibrium which teaches life forms changed suddenly from one form into another through massive random genetic mutations caused by massive radiation.

But of course, we’re talking about the “war” between gradualism and punctuated equilibrium. For the sake of brevity I will keep this part short, but for a more in depth understanding of the non-issue do read that infamous gradualist’s book Climbing Mount Improbable. All I will say on the subject is that this “war” really is not being waged. Every reasonable scientist understands both mechanisms and no one is exclusively in one camp or the other, it’s just a matter of which occurred more frequently and why. Either way the evolutionary process of random mutation and non-random selection remains undisputed, it’s just a matter of how quickly it certain events came about and how long a species went without evolving.

Imagine a fish with part fins, part feet with fins evolving into feet. What survival benefit would there be? The fish couldn't use its fins or its feet, and there are no fossils showing such a creature existed. They only exist on automobile bumper stickers!

Automobile stickers aside, there are plenty of fossils that demonstrate this elegant transition from fins to the tetrapod leg, and I will be happy to explain.

First of all, we are not looking at fish that magically jumped out of a pond and started to walk on the bare land. We are looking at a boggy environment; one where the distinction between where the land ends and the water begins is not so well defined as the edge of a swimming pool. This indistinct boundary gave several different niches, and not just the two of “water” and “land”.

The most watery niche would have been happily populated by swimming vertebrate fish, let’s call them species A. However, getting closer to the shore, there was a niche that was more murky, more shallow, and probably containing more debris from the vegetation that grew closer to the land. The original species A  would not have been able to inhabit this niche, there being too much crap in their way to swim properly, but a fish with slightly sturdier limbs would have been more adept at moving around the murkiness and pushing itself around the debris. Why would it want to? How is this advantageous? Well, perhaps this area is a great place to hide from predators, if their predators were also free-swimming creatures that would have had a difficult time getting around in the shallows. Maybe there’s a whole bunch of food that the animal likes to eat caught in these shallows, food that other weaker-finned individuals can’t get to. Either of these would give these animals with stronger fins a selective advantage over ones without, therefore natural selection could begin its work selecting for that trait.

Some time passes and now this murky niche is well populated with these sturdier-finned fish, now called species B. Getting closer to the shore, there is yet another niche just waiting to be populated, one with even more shallow water and larger debris, rocks and other such inconveniences. This new niche is still too hard to manage for our species B, but fish with even sturdier limbs could get around it, propping themselves up over the rocks and crap in order to slither past the large debris and into more protected pools with more food. This would again be advantageous, and natural selection would select for such a trait. We now have something that can be called a “half-fin half-leg” in our species C, because while it is still not strong enough to support the weight of the animal on dry land, it is still much more of a leg than the fin we started out from, being able to at least propel the animal over stones and wood in the water.

We have now arrived at the edge of the water. Guess how much food and protection being able to leave it would give! We now have all the makings of a good limb, it having gotten stronger and sturdier over evolutionary time, it just needs a bit more support. This new species of animal probably still reproduced and lived in the water, but it was able to make brief expeditions onto the land, much like modern amphibians do today.

What is the discussion between gradualism and punctuated equilibrium here? It has more to do with how quickly these events came about, how constant the rate of evolutionary change was over time. It does not have anything to do with the mechanism itself that I have described, which has evidence to support it. Not the least of which are transitional fossils:

Evolution is possible only if there’s information (genes) directing it. Only variations of already existing genes are possible, which means only limited evolution and adaptations are possible. Nature has no ability to invent new genes via random mutations caused by random environmental forces.

Contrary to popular belief, there is no scientific evidence that random genetic mutations caused by unthinking environmental forces such as radiation can or will produce entirely new genes for entirely new traits. Mutations only produce more variations of already existing genes. For example, mutations in the gene(s) for human hair may change the gene(s) so that another type of human hair develops, but it'll still be human hair!

Well that really depends on what you mean by “invent” and “new” now doesn’t it!

Genetic duplications happen often for a varitey of different reasons. Sometimes an error in the copying mechanism of DNA causes large chunks of it to be copied twice, and in these chunks of duplicated DNA there can be a gene that actually has a function caught inside. Now the organism has more copies of a gene than it needs to make an adequate amount of protein needed for its survival, so a mutation in this copied gene that might have been fatal to the organism can in fact happen in this duplicated gene with no harm done, seeing as the animal still has enough of the original protein to survive. This allows for more mutations in this gene to be passed on, since the animals containing them are not adversely affected and therefore can reproduce as well as the next guy. Occasionally, these mutations can cause the gene to create a different protein, one that folds in a different way and therefore can have a different function, and this new protein can give the animal that has it a selective advantage. One great example of this happening is seen in the Lenski experiments. Another is seen with the evolution in the lab of bacteria being able to digest nylon. When this happens, the mutated gene in question is referred to as a “new” gene, because it codes for a new protein that has a new function. As you can see, it is very possible indeed.

Because mutations are accidents in the genetic code caused by random environmental forces they're almost always harmful. They damage the genetic code similar to how the random energy from an earthquake damages a building. Even if a good mutation occurred for every good one there would be hundreds of harmful ones with the net effect, over time, being deleterious to the species, even causing extinction. Even "neutral" mutations will become harmful when enough of them accumulate and are passed on. Mutations may also trigger the duplication of already existing traits.

Actually, they’re almost always neutral, but even if they were almost always harmful this argument still makes no sense.

Let’s say that for every hundred mutations 99 are harmful and 1 is beneficial. Let’s say that mutations like these occur in 1 out of 10 animals. If you have a population of 1000 animals, 100 of them will have mutations. That means that 99 of those will die, and 1 will have a trait that is selected for by natural selection. Well, what the hell is the problem here?! You still have 901 animals around to mate and have babies, the ones born from the parent with the advantageous gene will be more likely to have more babies in the future, evolution by random mutation and natural selection happens. Random mutations are just that, random. The individuals that have the beneficial ones are not constrained by the ones that have harmful ones, they are free to evolve and mutate independantly of one another.

What about "Junk" DNA? The latest science shows that "Junk DNA" isn't junk after all! It's we who were ignorant of how useful these segments of DNA really are. Recent scientific research published in scientific journals such as Nature has revealed that the "non-coding" segments of DNA are useful, even essential, in regulating gene expression (how, when, and where in the body genes are expressed) and various intracellular activities. Just because these segments don't code for protein doesn't mean they're not useful or that they don't code for something else.

Gee, I wonder why he didn’t give us the reference to that revealing Nature article? Oh that’s right, because it doesn’t exist. I think he’s vaguely referring to recent discoveries in microRNAs and the like, but that doesn’t mean that there our genomes are still not largely composed of junk DNA. It just means that they have discovered a function for another teeny tiny percentage of our genome.

Many people have wrong ideas of how evolution is supposed to work. Physical traits and characteristics are determined and passed on by genes - not by what happens to our body parts, as Darwin believed. For example, if a woman were to lose her finger this wouldn't affect how many fingers her baby will have. Changing the color and texture of your hair will not affect the color and texture of your children's hair.

No asshole. The father of the Inheritence of Aquired Characteristics was Lamarck, not Darwin, and his hypothesis has been refuted as false since the 1800s. Catch up.

At this point he does gripe on about human evolution, but seeing as he links to another article where he supposedly talks about that in more detail, I’ll skip it here in order to approach it exclusively in another post.

Just a few more words from our friend before concluding this ever-growing response:

A true transitional form wouldn't survive. It would be unfit for survival. Remember the example of the fish with part fins, part feet? Natural selection would have eliminated any such forms of life, if ever they even got to that point!

Well yes, I do remember explaining how well those transitional forms got on! So let’s continue:

DO EYES CARRY SCARS OF EVOLUTION? Read this fantastic Internet article by biologist and creationist Brian Thomas. Thomas refutes every argument of a "flawed" design for the eye, and explains how and why the so-called flaw is actually the best thing for the eye.

Sorry, quoting a creationist’s internet dribble is not the same as giving a scientific source for your argument. But hell, if we’re allowed to link to people talking on the internet as opposed to hard scientific papers, I’ll let NonStampCollector explain the "scars of evolution" the human eye posesses.

He then goes on to whine about how real famous scientists wont talk to him. None of it is relevant to the topic at hand, but this little lie and argument from authority still stuck out:

Einstein didn't believe in a personal God like Christians do, but he did believe science pointed to the existence of an all powerful and intelligent Creator!

HA! Bullshit! Besides, even if it was true, so the fuck what? There were very intelligent people once upon a time that believed that the Earth was flat, but that doesn’t make it any more true today than it did back then, regardless of how smart or famous the person that believed it happened to be.

Let’s conclude now shall we?

I have given lectures defending scientific creationism before evolutionist science faculty and students at various colleges and universities. At the end, I opened up for comments, questions, rebuttals. Very few of the evolutionist science faculty criticized what I had to say, and, when they did, I successfully answered them.

OK, I may not be part of the faculty at my university (yet?) but I’ve answered you. I’d like to hear your “successful reply”.

Until then, I’ll take a look at the other articles he quoted on my video, try to put them in some kind of rational order by topic and rebut in the most concise and clear way I can. If anything I said was too concise and you would like further explanations please feel free to comment and ask me to elaborate.

It's Official, I Like This Guy

I keep humming my new favorite Christmas carol of all time, so seeing as I found a few spare moments I thought I'd watch a couple more of his videos on youtube. It is official, I really fucking like this guy!

Now before you feel like thrusting your hand in the air like a good pupil to point out all of the little mistakes he makes when describing evolutionary theory please give a little artistic liberty on this one, it's a stand up routine with a funny conclusion not a fucking science lecture!

And we must conclude with this little nugget of purely offensive-and-yet-really-not-offensive-at-all fun
(animations done by someone else of course)

Yup, it's official. I really like Tim Minchin

Repost: The Missing Link Fallacy

Well today is the last day of vacation for me, getting a little blue seeing as it also marks the first day that I will be living alone for the next two years at least, so I thought I'd cheer myself up in looking over some excellent blogposts that I just love. Here is a little beauty brought to us by Oliver Knevitt over on Science 2.0 that I just loved. While I can fully appreciate how eye-rollingly annoying it can be to be swamped by young-earth creationists, this well measured takedown is not only great for sticking yet another nail in their now more-metal-than-wood coffins, but also simply explains an aspect of evolutionary theory that many people just don't understand or know. So, I hope you like it

The Missing Link Fallacy

The comments thread for an article that I wrote a couple of weeks ago has suddenly been swamped by the replies of a young-earth creationist. Perhaps I should have expected it, with an article about hoaxed fossils. He presents an orgy of anecdotes that he claims (I assume it's a he) debunks my evolutionist agenda.

I say orgy: its a bacchanalian romp of differing misconceptions and twisted logic - basically, nothing out of the ordinary for a creationist, for whom apparently the addition of even more terrible ideas can only strengthen your argument. Very quickly, I got bored of the tedious process of writing a comment correcting these misconceptions, and I was just about to ignore it and start writing my next article.

That is, until circularreason, showing a surprising amount of humility, said

I would like to hear your thoughts on the fallacy of missing links, I am reasonable and willing to listen.

Now, there is something that I am willing to bend on. You see, missing links, or rather, the apparent lack of them, are something that is bandied around irritatingly commonly on rant-threads like these. Their alleged absense is something that many creationists believe represent the nail in the coffin for evolution, and creationists act as if it is something that us paleontologists are all embarrassed about, fervently collecting in the desperate hope that one will turn up.

But, of course, this is absolute rubbish, and their insistence on using such arguments only does more to highlight their complete lack of any understanding of evolution, as I will outline here.

(I warn you, I lost an entire afternoon of work typing it, and it ended up being bit of a monster of an article!)

Snakes and ladders

The first major reason for this misconception, I think, is part of a global misunderstanding about evolution in general. In their understanding of evolution, many people - non-creationists included here - imagine in their heads something akin to the classical idea of "The Great Chain of Being". Here, all life is connected by a great ladder of increasing complexity; from the lowly worms and snakes at the bottom, up through the animals, to humans, then to the angels and then, almighty God at the top. Its an idea that was commonly hijacked to justify the inequality in society and the divine right of kings, and eventually laid the foundations for linnean taxonomy.

Whilst nobody would claim to believe in such an idea these days, dating as it does from the time of the Greeks, most people in their mind's eye see some version of this story. Many understand macroevolution by envisaging a grand procession of life, where all creatures, through time, climb inexorably up this ladder, finishing with the the proud human, the most evolved of all beasts.

This is an unfortunate misunderstanding. I find myself speaking to a large amount of people who are genuinely surprised when I tell them that we didn't evolve from chimpanzees. They think I'm winding them up when I tell them that there's no such thing as the missing link between chimpanzees and humans, simply that we share a recent common ancestor with them. This common ancestor is likely to look similar to the two of us, but it need not be.

Evolution, then, is not a ladder. It's not even a tree. It is a thick, tangled bush, with no up and down. All we see today is the continuously growing ends on the twigs of this bush, which can split and slowly diverge. We can only have missing links if we have a chain, whereas what we really have is ends, with missing twigs. Hence no missing links.

Even the idea of a tree, with increasing complexity upwards, is wrong. Yes, many groups are characterised by increasing complexity, but many are characterised by an increasing loss of complexity. Some may lose an entire life stage. It's still progress, but not necessarily in the "upwards" direction. No living animal is more evolved than anything else, it may have simply evolved to retain its primitive characters.



But perhaps I am being pedantic - or semantic, anyhow. It is, of course, true that there are such things as transitional forms. By this, we mean that lineages can slowly accrue changes in their morphology through time. It is perhaps this concept that many refer to, rather than a chain of being as such. Maybe if people referred to transitional fossils it wouldn't irritate me so such.

Transitional fossils...?

A cladogram of dinosaur evolution.

We are not out of the woods yet, though. The likelyhood of finding a fossil that represents an ancestor of any sort of other organism, a member of one of those queues of organisms between known organisms on a cladogram, is astronomically low. The chance is even lower when we look very deep into the fossil record - so much so, that we have almost certainly never found one.

Surprising? It shouldn't be - think about it. Groups of organisms are continually evolving, groups migrating, changing, constantly splitting from one another in a fractal way. Are we really likely to accidentally stumble across one particular animal that is a member of a group that is a direct ancestor of another group we know about? No, of course not.

We have to image the lines on a cladogram as being a zoomed out line of our ancestors, a long queue stretching back towards our common ancestor with the next twig. Its along these lines that we slowly change. If the organism bears a resemblance to another or seems to be transitional, it could well be on a myriad of small offshoots from our line of ancestors, and could even be close to our line, but the chances of it actually being on our line is tiny. Walking through an old graveyard, are any of the gravestones likely to be an ancestor of yours? How about a skull in an African cave? Or a fossil monkey in a swamp? Even taking into account pedigree collapse, its still highly unlikely.

Transitional fossils do exist. Its just that they aren't necessarily the precise ancestors of organisms that we see; rather, are members of a cloud of organisms treading along some of the same evolutionary ideas, being as they are closely related to one another. Out of this maelstrom of different lineages there may be just one thread that gives rise to another important lineage. The fossils in this cloud still give us a chance to test our hypotheses about how the trends may have occurred in the lineages we're interested in. But they may not necessarily a true link in the chain.

That's the true art of paleontology, you see: using examples from the fossil record to infer trends and to test hypotheses about the nature of evolution. To assume that it is simply trying to make a sort of flip-book of evolution through time is incredibly ignorant.

Zeno's paradox

Tetrapod evoltuion: too many transitional fossils

A particularly egregious taunt often flaunted by creationists is "Give me just one missing link fossil and I will believe you". It's particularly loathsome because as soon as you present said creationist with a perfectly decent transitional fossil, they demand a link between those three fossils. And now there are two gaps to be filled with more missing links. Like the distance between Achilles and the tortoise in Zeno's paradox, this continues ad infintum.

How many fish to tetrapod intermediates do you want? Like it or not, the bigger problem that tends to be encountered more often in paleontology and related disciplines these days is that there are far too many plausible ancestors to place on our cladogram. The difficult bit is deciding which of these are closer to us and which are further away.

Mosiac evolution

Another related irksome point is the the very unitary approach taken to organisms. Whilst it is true that the unit of selection is at the organismal scale, the body parts that evolve may be at different rates. This concept is known as mosaic evolution, and is at the basis of modern cladistics (the possession of the most derived body parts, the synapomorphies, define the group as a whole).

For example, in human evolution, bipedality evolved very quickly but large brain size evolved slowly and later on. So we will never find a fossil with both a mid-sized brain and an average adoption of bipedality; its just not how it happened. Similarly, we wouldn't necessarily expect the transitional form between maniraptors and birds to be something with medium length claws, medium length tail and legs and slightly asymmetric wing feathers. Archaeopteryx exemplifies this, with its mix of more bird like features, like a wishbone and asymmetric flight feathers, with more primitive characters, like a long tail and legs.

Macro to micro

Peter Sheldon's landmark study of welsh trilobites is a great example of gradual evolution in the fossil record

Many creationists these days seem to have quietly abandoned their objection to evolution at small scales. God knows why, but I presume its because the ark would sink with the sheer weight of beetles, molluscs and lice (every animal would of course have to be infested with every sort of parasite imaginable, of course). To do this, they seem to have invented a dichotomy between macroevolution and microevolution, envisaging them as different processes. They are both valid terms in evolutionary biology, but both at heart driven by the same inherent processes at viewed at different scales, and thus the dichotomy is false in this sense.

Where am I going with this? Well, all I mean to say is that; acceptance of microevolution is a wise thing, because there are cliffs worldwide stacked full with transitional fossils, if you accept evolution at the species level.

Rocks worldwide are dated relative to others by the gradual change of the constituent fossils that make them up. Unless you want to dispute the most basic tenet of geology, namely that the rocks on top are younger than those underneath, you cannot dispute that these organisms are slowly changing through time. Gradual evolutionary change has been noted in trilobites, bryozoans, bivalves, you name it. Its just that, because these organisms are marine, small and shelly, they have an exceptionally good fossil record.

If we had a similarly good record for, say birds and maniraporan dinosaurs, it would truly be a wonderful thing. But think how lucky we are to be able to say what we can about bird evolution. How fortuitous that those Archaeopteryxes should have died and fell in a stagnant lagoon? We may not have as good a resolution as we do for shelly marine critters, but we can still make out the general trend.

A god of the gaps

How about the many distinct gaps in the fossil record though? Is god quickly changing the organisms for more complex ones?

Asides from the large gaps due to pauses in sedimentation, it is true that in many sedimentary columns, a group may appear, then disappear entirely and be replaced with something different, with little sign of transitional forms between them. Hesitantly then, I'll drag punctuated equilibrium theory into the fray, kicking and screaming because of all the times it gets misrepresented and misunderstood.

The way it works is that, at this scale, it is expected that any evolving will be done elsewhere. Natural selection generally acts to stabilise forms, trimming gaussians of character distribution at the edges like neat topiary bushes. So, a form may generally stay the same for a long period of time. If, however, a splinter group of random organisms gets separated and ends up elsewhere, they will gradually diverge from the rest. This is either because of different ecological niches being available, or simply through a lack of being able to recombine your genes with the rest of the group - a bit like the way that dutch-speaking people can no longer understand afrikaans, even though the two languages were once the same thing. And like when dutch people visit south africa on holiday, once the two are reintroduced they are no longer compatible. But, crucially, because the evolution of the splinter group occurred elsewhere, there is no record of it in the sedimentary column, and hence the transitional forms are elsewhere. And, given the incompleteness and geographical bias of the fossil record, they are likely to be unseen.

My worry about introducing Punc-Eq is because it is often thought about as some sort of ad-hoc, deus-ex-machina argument; a cover-up story. Let me say it clear: Punc-Eq is not some sort of excuse. Nor is it the rule. Punc-Eq has been conclusively proved by a study on bryozoans, as has gradualism; the two occupy a continuum, and the results of multitudinous studies done on it have formed a general theory of microevolution. There are, I'll admit, many gaps in our understanding of the way it works, but as with all science, that's the fun bit.

The point to draw from all this, if you haven't understood any of the above explanations, is that the need for transitional fossils, at all scales, is simply not there. They are of course, handy, illustrative of processes, and provide the most direct proof of our hypotheses, but they are by no means the only means of proof that two lineages are related.

Was there a point to me typing up this monster of an article?

Wouldn't it be great if a creationist read this and thought: "Hmmm. It appears I have been mistaken for all these years, and I think maybe it's time to join the world of logical thinking". Wouldn't it be great if just one person did that? Will circularreason change his mind?

Depressingly, I doubt it very much, and that's the very reason why I am generally reticent to answer creationists. But I'd like to think that, at least I can provide reassurance for anybody teetering on the edge, worried about whether the lack of transitional fossils is something that keeps paleontologists awake at night, and considering converting to the dark side.

So, to this person, then; re: the lack of missing links: Don't worry, we've got it covered.