The Logic of Science

Many people are under the false impression that evolution is just a guess or a belief, when in reality, it is one of the most well-supported concepts in all of science. The evidence for it is overwhelming and comes from many different disciplines such as paleontology, comparative anatomy, biogeography, and perhaps most significantly, genetics. Indeed, modern genetic tools have allowed us to repeatedly test evolution’s predictions, and those predictions have consistently come true. Therefore, I am going to explain in simple terms what the genetic evidence is and why it is so compelling. As I will show, the evidence perfectly matches the predictions that the theory of evolution made decades before we could test those predictions. Further, the patterns do not make sense if our modern organisms were specially created, because there is no reason why a creator would have had to make life with these patterns. In other words, if you want to say that God created our modern organisms, then you are left in the awkward position of arguing that out of an infinite range of possibilities available to him, God chose to create life in the one and only way that would be consistent with the predictions of evolution.

Note: Throughout this post I will use the term “creationist” to refer to people who deny evolution. There are many sub-categories within that, and there are also Christians who accept both evolution and the Bible (theistic evolutionists). I am not attacking Christianity or religion here. Rather, I am simply explaining why the evidence overwhelmingly supports evolution and refutes creationism.

 Note: I am going to talk about relationships based on genetic similarities and shared genetic traits throughout this post, but please realize that I am doing this for simplicity. Actual phylogenetic studies employ rigorous statistical analyses to look not just at the proportion of shared DNA, but also at parsimony and various other factors. So I am being simplistic to avoid losing anyone, but the actual science is more complex, and the more that you understand it, the clearer it becomes that evolution is correct.

That basics that everyone agrees on

To start this post, I need to explain the most basic concepts of how we use genetics to assign evolutionary relationships, and the easiest way to do that is with human families. Imagine that you gave me blood samples from yourself and five relatives, all of whom were in your generation. I then extracted and sequenced the DNA from those samples, and I found that there was one person whose genetic code was very similar to yours but more different from the other four samples. Thus, you two share a substantial portion of the variable regions of your DNA. From that, I would conclude that you two share a more recent common ancestor with each other than with your other relatives. In this case, that ancestor would probably be your parents (i.e., you’re probably siblings). This should make good sense. You obviously got your DNA from your parents, as did your sibling. Thus, since you both got your DNA from the same source, we naturally expect your genetic code to be more similar to your sibling’s than to the codes of people who have different parents.

As I look at the data further, I also find another pair of two individuals who are more similar to each other than they are to either you or your sibling, thus suggesting that they share a recent common ancestor (their parents) that you do not have. However, both of them are more similar to you and your sibling than they are to the final two relatives. This would suggest that you and they share a recent common ancestor that is not shared by the final two relatives (e.g., you’re cousins who share grandparents). Finally, the last two individuals are again closely related to each other, but they are more distant to the rest of you. This would suggest that the six of you have a more distant common ancestor (perhaps you share a great grandparent).

This is an example of a cladogram (aka phylogenetic tree) showing the relationships between you and your five relatives in my example.

As you can see, we can use those genetic data to reconstruct your family tree (what we like to call your phylogeny), and we can illustrate it using a phylogenetic tree or cladogram like the one on the right. On these diagrams, vertical lines represent common ancestors. Thus, you can see that you and your sibling share a recent ancestor (your parents), and you, your sibling, and your cousins share an ancestor slightly further back (your grandparents), and all six of you share an ancestor even further back (your great grandparents). Again, this should all make good sense when you think about how DNA is passed. All six of you share a certain amount of DNA because you all inherited it from your great grandparents. After that, however, things began to diverge. One of your great grandparents’ children went on to become your grandparent, while another one went on to produce your more distant relatives. Thus, you, your sibling, and your cousins are more alike because you all received DNA from the same source (your grandparent). Then, one of your grandparents’ children went on to become your parents, while another became your aunt/uncle and produced your cousins. Does that make sense?

I want to pause here for a moment to make a crucially important point. In my example, we did not need actual DNA from your ancestors. Rather, we were able to infer their existence from the patterns that we saw in the DNA from the current generation. This is a very important strength of genetic analyses: we can use data from the current generation to infer the existence of past ancestors.

Broadening the scope

Everything that I have said thus far is universally accepted. No one disagrees that these genetic tools can determine family relationships like this, and even the most die-hard creationist would have no problem with what I have said. However, the power of these tools doesn’t stop there. We can also use them for an entire species. For example, we can trace the ancestry of all humans back to a common source. Here again, creationists have no problems. They agree that these methods are reliably showing true relationships, and it’s not simply a case of some people happening to have similar DNA. They agree that the similarities are similar by descent and indicate common ancestry (i.e., they accept that these methods can reliably identify ancestors that we do not have DNA samples from). In other words, they agree that these are actually showing real, evolutionary relationships within people (they would argue that the tree goes back to Noah and his family as the common ancestor).

We can, however, go even further than just a species, we can also use it for complex species with many breeds (such as dogs) or even for entire families of animals (in the scientific classification of organisms, family is the third most specific classification, followed by genus and species). We can, for example, show that all species of ducks (family Anatidae) descended from a common ancestor. We can also show that all tree frogs (family Hylidae) share a common ancestor, all pythons (family Pythonidae) share a common ancestor, all kangaroos (family Macropodidae) share a common ancestor, etc. Again, creationists are OK with this. At the family level, they agree that these methods are showing true relationships. You see, young-earth creationists argue that on Noah’s ark, Noah did not take two of each species, but rather took two of each “kind,” which they arbitrarily define as being roughly equivalent to scientists’ term “family.” Thus, they agree with these data, because they think that all modern ducks descended from a single pair of ducks on the ark, all modern tree frogs descended from a pair of tree frogs on the ark, etc. I have even seen some of them go as far as saying that the genetic evidence within families is evidence of creationism/Noah’s Ark (that is a logical fallacy known as affirming the consequent).

Cladogram of dog breeds. Figure 1a from vonHoldt et al. 2010.

Creationist’s disagree, however, the instant that we start extending beyond the family level. Take marsupials (pouched mammals) for example. Using these genetic techniques, we can tell that many carnivorous marsupials, like Tasmanian devils and quolls, are all in a single family (Dasyuridae) and share a common ancestor. Creationists are fine with that, and agree that the methods are showing true relationships. However, we can use exactly the same methods to broaden the scope just a little bit further and show that members of Dasyuridae are more closely related to the Myrmecobiidae family than they are to any other living marsupials. Thus, we can tell that Dasyuridae and Myrmecobiidae evolved from a common ancestor, and we group them together into the order Dasyuromorphia (order is one step broader than family). At that point, creationists suddenly disagree. Suddenly they insist that these methods are just showing similarities, not true relationships. They are even more upset when we use exactly the same techniques to show that the order Dasyuromorphia evolved from the same common ancestors as the orders Notoryctemorphia and Peramelemorphia (Gallus et al. 2015). Further, we can keep going with this until eventually we have a cladogram for all marsupials that shows that all of them share a common ancestor and are more related to each other than they are to other mammals (just like you are more related to your sibling than to your cousins; Cardillo et al. 2004).

A phylogenetic tree of several marsupial families. Figure 7 from Cardillo et al. 2004.

We don’t have to stop there, however. We can continue to use the same methods to show that all mammals share a common ancestor, all animals share a common ancestor, and ultimately that all life on planet earth evolved from a common ancestor. Creationists, of course, object to this in the strongest possible terms. They insist that these genetic similarities aren’t actually showing real relationships, and they are adamant that the fact that two groups share more DNA with each other than with some other group doesn’t indicate that those two groups evolved from a common ancestor. As you can hopefully now see, however, that argument is logically inconsistent because it is completely and totally arbitrary to say that these methods work within families, but don’t work for taxonomic levels higher than that. That reasoning is logically invalid and completely ignores the evidence. Look at the cladogram above, for example. It shows some of the relationships that I described in marsupials, and I have colored the parts that creationists agree with green and the parts that the disagree with red. As you can see, within each family, they accept quite a few common ancestors. They agree that these methods can reliably show ancestry, yet as soon as we move beyond the family level, they say that the methods don’t actually show common ancestry. They agree, for example, that all members of the genera Dasyurus, Neophascogale, and Phascolosorex descended from a common ancestor, yet they disagree that the families Dasyuridae and Myrmecobiidae descended from a common ancestor. That belief is completely arbitrary and has no scientific basis or logical credibility. To put this another way, look at the clodagram that I showed earlier for dog breeds (which creationists have no problems with), then look at the cladogram below for all life on planet earth, and tell me what the difference is. Explain to me why we should accept that these methods work for dogs but arbitrarily believe that they don’t work for higher taxonomic levels.

Phylogenetic tree of life on planet earth. Via the University of Texas.

Extraordinary predictions

I want to take a minute here to try to impress on you just how extraordinary these genetic results are. Scientific theories are often judged by their predictive power. In other words, good theories are ones that can accurately predict the results of future experiments, and the more extreme the predictions, the better. In this case, the theory of evolution made the astounding prediction that we should see these genetic patterns decades before we actually had the ability to test them.

When Darwin first proposed the theory of evolution, genetics were unknown. No one knew what DNA was or how traits where inherited (see note). In fact, Darwin himself was totally wrong about how inheritance worked (he subscribed to the “blending” hypothesis wherein the traits of two parents blended together). Nevertheless, despite being wrong about the mechanism, it was clear that there had to be some way that the information for traits was passed from parents to offspring, and if evolution was true, then scientists realized that the information should record evolutionary history. In other words, if evolution was true, it should be possible to use that information in exactly the way that I described to show that all life traces back to a single common ancestor.

That was already an extreme prediction, but it didn’t stop there. You see, it wasn’t enough for there to be a pattern. Rather, the pattern had to match overarching morphological patterns. In other words, it had to show that all of the parrot families share a common ancestor, all frogs share a common ancestor, all marsupials share a common ancestor, etc., and that is exactly what we find. Further, this pattern had to match the fossil record, which is where things get even more extraordinary. You see, it may make intuitive sense to you to expect that all frogs would be genetically similar, even if they were specially created (more on that later), but why would genetics show that modern amphibians and modern reptiles share a common ancestor? That’s not something that you would expect under creationism, but it is what evolution predicted, because the fossil record clearly showed that both modern amphibians and reptiles evolved from ancient amphibians. Thus, evolution predicted that modern amphibians and reptiles should share a common ancestor.

Similarly, the fossil record showed that amphibians evolved from fish, and that both mammals and birds evolved from reptiles. Therefore, if those fossilized patterns are correct, we should see the same patterns in DNA, and we do! Think about how amazing that is. Evolution predicted the existence of an extremely precise pattern long before we could test that prediction. If evolution isn’t actually true, then you have to say that the patterns that we see in morphology, the fossil record, and genetics just happen to perfectly match up. That’s insane! Further, let’s be clear that I am only naming a handful of the predictions here. They also extend to all plants, bacteria, archaea, invertebrates, and other chordates. We are talking about thousands of predictions that evolution nailed! That is extremely strong evidence that evolution is correct. To put that another way, what are the odds that evolution would have gotten all of those predictions right if evolution wasn’t actually true?

Crocodiles are more closely related to birds than other reptiles. Image via Green et al. 2014.

To really drive this home, let’s talk more about birds for a minute, because their story is incredible. As I explained in a previous post, there is a ton of fossil evidence showing that birds evolved from dinosaurs. We have lots of transitional fossils showing that this occurred. Further, the fossil record shows the existence of a large phylogenetic group known as archosaurs, which included both ancient crocodilians and the group of dinosaurs that evolved into birds (more details at the University of California). This tells us that crocodiles and birds should actually be each other’s closest living relatives, and it leads to an absolutely incredible prediction. Genetically, not only should birds fall out as reptiles, but crocodiles should actually be more closely related to birds than they are to other reptiles. That is an amazing prediction that makes no sense under creationism. Why would God give crocodiles a genetic code that shares more in common with birds than other reptiles?

As you might have guessed, however, this prediction totally came true! Genetically, birds are actually reptiles, and crocodiles share more DNA with birds than with other reptiles (Green et al. 2014)! Again, this is because birds and crocs share a common ancestor (just as you and your sibling are genetically similar because of a common ancestor). If you stop and think about this for a second, it is mind-blowing. Genetically, crocodiles are more similar to birds than they are to other reptiles. If that doesn’t make you question everything, then I don’t know what will.

Note: Technically, Gregor Mendel (who discovered how genetic inheritance works) was Darwin’s contemporary, but Mendel’s work was largely unknown until well after his death.

Functionally arbitrary similarities

At this point, you might be tempted to think that these genetic patterns are there by necessity. For example, you might think that all frogs have similar genetic codes simply because they all have to have similar codes in order to have the characteristics of a frog. Thus, you might think that these genetic patterns are functionally necessary and would have to exist even if modern organisms were specially created. There are, however, numerous problems with that line of reasoning.

First, that argument would only have the potential to apply to the patterns within fairly narrow taxonomic units, and it would not explain the overarching patterns. In other words, the fossil record tells us that modern amphibians evolved from ancient fish, modern reptiles evolved from ancient amphibians, modern mammals evolved from ancient reptiles, birds and crocodiles both evolved from an ancient archosaur (reptile), etc. As I have already explained, genetics show us exactly the same progression, and there is no reason why that pattern had to exist. An all-powerful being could easily have created birds, reptiles, amphibians, mammals, etc. without making this pattern. Indeed, he could have created life such that each “kind” was unique and did not show any patterns of relatedness to the other “kinds.” To put this another way, why did God make crocodiles more similar to birds than to turtles?

Second, even within more narrow taxonomic groups (defined by morphology in this case), there is still actually no need for the level of genetic similarities that we observe. As I will explain, the genetic code is remarkably redundant and pliable, and you can have two very similar organisms with very different genetic codes and evolutionary histories (conversely, you can also have two very different organisms with comparatively similar genetic codes, think about crocodiles and birds again). I will explain more details about how that works in a moment, but let me give you the big picture first. There is a process known as convergent evolution wherein similar habitats and life histories cause two distantly related species to evolve to have similar morphological or physiological traits, but because they evolved independently, their genetics are quite different.

A sugar glider (left) and flying squirrel (right). Despite appearing similar, they are actually very distantly related, and each species evolved to be similar via convergent evolution.

Sugar gliders (Petaurus breviceps) and northern flying squirrels (Glaucomys sabrinus) provide a really nice example of convergent evolution. As you can see in the image, they look extremely similar, and they both possess remarkable adaptations such as a large flap of skin that they can use to glide, a large bushy tail to steer with, large forward-set eyes for good night vision, etc. If you didn’t know any better, you would probably think that they are close relatives, but you’d be very wrong. You see, sugar gliders are marsupials, whereas flying squirrels are placental mammals. So genetically, flying squirrels are far closer to you and me than to a sugar glider, and sugar gliders are far more related to kangaroos than to flying squirrels. Nevertheless, despite having very different genetic codes, they have very similar morphology (with regards to the adaptations for gliding) because they both adapted to similar habitats/life styles. There are tons of other examples like this that I could give, but hopefully you see my point: there are often multiple ways to achieve the same basic outcome, and you don’t need to have similar genetics to be morphologically similar.

Note: Lest anyone try to say that this example actually discredits evolution because it shows that morphology and genetics don’t always match up, there are other traits that distinguished them long before genetics (e.g., the pouch), so this was not a case of morphology and genetics disagreeing. Nevertheless, my point stands that both species evolved many of the same traits in different ways, and different genetic codes can achieve the same outcome.

 So why is it that the genetic code is so malleable? Why can organisms with different genes evolve the same basic structures? To answer that, you need to understand how DNA works. It consists of four base pairs (represented as A, T, C, and G), and those bases are arranged in groups of three, with each group coding for an amino acid. The arrangement of those amino acids then determines what proteins are formed. Thus, a string of DNA codes for a series of amino acids which in turn forms a protein. That code is, however, highly redundant, and several different groups of bases can form the same amino acid (and therefore same protein). For example, the amino acid proline can be formed by the codes CCT, CCC, CCA, or CCG. They all form the same amino acid, and therefore, the same subsequent proteins. Indeed, most amino acids can be formed by at least two different sets of bases. Therefore, because proteins are formed from strings of numerous amino acids, you can have tons of organism all producing the same protein, but doing so via different genetic codes (there is also redundancy in the proteins themselves in that you can swap some amino acids and still get the same basic protein, this does have an effect on the function of the protein, but not a significant enough one to really make creationists’ argument persuasive).

Additionally, large portions of the genomes of most organisms are what are referred to as “junk DNA” (Rands et al. 2014; ENCODE Project Consortium). Exactly what these are and what they do is still the subject of much debate, but it does appear that they are not actively coding nearly as much as regular DNA (if at all), and mutations in those regions are unlikely to have large impacts on organisms. Indeed, when you combine the presence of junk DNA and the redundancy in the genetic code, it turns out that for many species, most mutations are actually “neutral” and have no effect on the organism (Eyre-Walker et al. 2007).

The consequence of all of this is really important. It means that there can be a lot of variation in genetic codes without it affecting functional traits (or in some cases, with it only have minor affects). In other words, an omnipotent, all powerful being could easily have designed two organisms that were nearly identical in morphology and physiology, but had extremely different genetic codes. To put that another way, as it turns out, it is not at all necessary for two species that look and behave like frogs to have similar DNA. To be clear, there certainly are conserved sections of DNA, and some sections of the genetic code are similar for functional reasons, but there is no reason why the similarities should consistently extend across the entire genome. Because of the redundancies in the genetic code, you could easily have two “frogs” with radically different genetics. Indeed, it would be entirely possible for an all-powerful all-knowing God to make four identical “frogs” one of which had protein sequences that matched those of birds, one of which had protein sequences that matched those of fish, one of which had protein sequences that matched those of reptiles, and one of which had protein sequences that matched those of mammals! Lest you think that I am pulling your leg, think about birds and crocodiles again. They are extremely different organisms with similar genetic codes.

“God did it”
I want to conclude this post by talking about the most common response that I get to all of this. More often than not, when I present this evidence to a creationist, I get the following reply, “well, those patterns are just the way that God created everything, and the common patterns exist because of a common creator, not because of a common ancestor.” There are, however, numerous problems with this response, so let me lay them out for you.

First, as I explained at length earlier, this response is logically inconsistent. If you agree that genetics show true relationships at the family level (as all creationists seem to), then you cannot arbitrarily say that they don’t work at higher levels. That is not valid reasoning.

Second, this response is what is known as an ad hoc fallacy. It is a logically invalid cop-out that is not falsifiable (thereby violating a key requirement for science) and would never be accepted by anyone who wasn’t already convinced that creationism is true. You might as well propose that Barney the dinosaur is actually a real magical dinosaur who created these patterns just to screw with us. Just like the “God did it” response, I technically can’t disprove that claim, but it is clearly not a rational argument.

Third, this response has serious logical problems because of the nature of the genetic code. There are several parts to this, but first I want to address the one that I haven’t talked about yet, and it is easiest to do that by way of example. Like most modern scientists, I have been forced to learn some computer coding, which I use to write codes for organizing and sorting data, running statistical models, simulating data, and even making fictional examples for this blog. I am, however, a pretty horrible programmer. My codes always work in the end, but they tend to be clunky, inelegant, and redundant. Further, frequently when I need to code something, I simply take an existing code and modify it. That saves me time, but it generally produces codes with irrelevant lines that are left-overs from the codes’ original functions, as well as unnecessarily complicated processes that would have been far simpler if I had started from scratch. In contrast, someone who knew what they were doing and built each code from scratch, would be able to make codes that do exactly what mine do, but theirs would be very elegant and free of redundancies and irrelevant lines of code.

It may seem like I am off topic here, but computer codes are actually remarkably analogous to genetic codes. Zeros and ones tell computers what to do in much the same way that As, Ts, Cs, and Gs tell organisms what to do. Now, ask yourself this question, if all life was created by an omnipotent, omniscient God, would you expect elegant, well-written codes that were free of redundancies, or would you expect clunky, bulky codes, that were hodgepodged together from existing codes and are full of redundancies and lines that no longer do anything? I would certainly expect the former, but what we find is the latter. The more that we examine organisms’ genetic codes, the clearer it becomes that they were made by randomly modifying existing codes, rather than writing new codes from scratch. That is why we end up with large non-functional (or barely functional) regions and codes that carry over from one group to the next. To put it simply, if God specially created modern organisms, then he is a terrible programmer.

This brings me to my final point, which is probably the most important one. As I have tried to make clear throughout this post, the genetic patterns that we see among organism are exactly what evolution predicted at every level. The relationships and patterns within groups are exactly what evolution predicted, and the overarching patterns of relationships among groups are exactly what evolution predicted. We are talking about thousands of predictions that evolution consistently got right. Further, as explained earlier, these patterns don’t have to exist for us to have organisms that look and function like our modern organisms. An all-powerful, all-knowing being could easily have created modern organisms such that there was no pattern at all. He could have scrambled protein sequences such that, for example, some bird proteins matched frogs, others matched fish, others matched reptiles, others matched trees, etc. Alternatively, he could have made extremely inconsistent patterns. He could have made some birds appear to be related to reptiles, others to fish, others to amphibians, etc. He even could have made a consistent pattern, but one that didn’t match evolution’s predictions. For example, he could have given all birds protein sequences that most closely match fishes. Any of those patterns would have been absolutely devastating for evolution. Anything other than exactly the pattern that we see would have falsified our understanding of life on this planet.

My point here is simple, if you want to say that God created all life on planet earth, then what you have to say is this: God (who according to the Bible is a God of truth, not deception) had a nearly infinite number of options for how to create life, yet out of all of those options, he chose the one and only pattern that would confirm the theory of evolution. To put that another way, life looks like it evolved. You absolutely cannot say that the evidence doesn’t support evolution, because evolution’s predictions have consistently come true. You can choose to ignore the evidence, but you cannot deny that it perfectly matches evolution’s predictions. So, you are left with saying that life on planet earth looks exactly the way it would if it evolved, but it didn’t actually evolve, God just created it in the one and only way that would make it look like it evolved.

In closing, I would like to ask you a simple question. If you are going to write off these genetic patterns as “just similarities,” if you are going to ignore this overwhelming evidence and these astounding predictions, then what would convince you that evolution was true? If the fact that it accurately predicted the genetic patterns of all living things isn’t enough for you, then what would be? What would it take to convince you that you were wrong?

Note: Some creationists try to contest arguments like this by pointing to cases where scientists have disagreed about how two groups of animals are related. There are, however numerous problems with that counterargument. First, in the modern genetic era, those debates usually only occur for pretty narrow taxonomic boundaries, while the overarching patterns remain undisputed. Second, those debates arise from one of two things: unclear morphology or unclear genetics. To put that another way, often what happens is that scientists are working with incomplete fossils and it is difficult to use them to determine how things are related. Thus, disagreements arise not because evolution was wrong but simply because scientists are working with incomplete data sets that have been preserved for millions of years (convergent evolution can also sometimes confound things even for living organisms). Other times, this arises from using a limited number of genetic markers. Sometimes, genetic patterns are hard to decipher, particular if you are only using a tiny portion of the genome, and these tools aren’t perfect, but as more and more studies are done using more and more markers, the picture becomes increasingly clear, and it overwhelming matches what we expect to see from evolution.

Related posts

• Can Science Tell Us What Happened in the Past? Historical vs. Observational Science
• Debunking creationism: a visual comparison of “micro” and “macroevolution”
• Debunking the creationist myth that mutations don’t produce new and useful information
• “If evolution is true where are the missing links?”
• Reducing irreducible complexity
• Sinking Noah’s Ark Part 2: The Order of the Fossil Record Confirms Evolution’s Predictions

References

• Cardillo et al. 2004. A species-level phylogenetic supertree of marsupials Journal of Zoology 264:11–31.
• ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 48957–74.
• Eyre-Walker et al. 2007. The distribution of fitness effects of new mutations. Nature Reviews Genetics 8:610–618.
• Gallus et al. 2015. Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analysis. Genome Biology and Evoltuion 4:985-992.
• Green et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346.
• Rands et al. 2014. 8.2% of the human genome is constrained: variation in rates of turnover across functional element classes in the human lineage. PLoS Genetics 10:e1004525.
• vonHoldt et al. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464:898-902.