The limits of science

Jerry Coyne has a post about the NCSE enabling woo, but there’s one part near his introduction that really stood out to me.

This accommodationism is most annoying when the NCSE assumes its science-has-its-limits stance, a stance designed to show that beyond those borders lies the proper and goodly realm of religion. Yes, of course science has some limits—it can’t (yet) explain why I love the paintings of Kandinsky and others find them abstract and boring. But how on earth do these “limits” somehow justify belief in the palpable nonsense of faith?

Going by his use of the word “yet”, it sounds like he doesn’t see science as being limited in theory. His post doesn’t focus on this point, so it isn’t entirely clear if that’s his position. However, it is my position.

Science is not limited in and of itself. It can tell us absolutely everything about the Universe. That includes telling us why we think something is beautiful or moral or why we love someone. Science is not theoretically limited in any way from being able to tell us all these things. The problem, however, that arises here is the whole “yet” thing. It causes confusion. Let me explain.

Science is limited in telling us a vast majority of things we might want to know. Right now it cannot tell us why we make all the choices we do or why some of us might find the ocean beautiful. But that is not a matter of science being limited in and of itself. In actuality, the limit comes from human ability, a lack of technology, a lack of necessity, the short span of time in which one person will live, the short time the entirety of the human race has and will exist, etc. We limit science; science does not limit us.

Repost: Only in the light of evolution

There are two reasons I want to make a repost of a post from about a year and a half ago. First, it’s always interesting to go back and read old posts for me. From time to time I have no recollection of making a certain post, so when I see it, it’s almost like it’s brand new to me. I do happen to remember this one very clearly, but it is at least understandable why I was skimming posts from May 2009. Second, I average significantly more views now than I did a year and a half ago. I feel this post is a pretty important one, and now that more people can see it, I would like to throw it back up.

~~~

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

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

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

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

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

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

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

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

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

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

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

Only in the light of evolution 3

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

There is a pattern within Life that can be seen on oceanic islands. Species which are present are often endemic – only found in that one location. The species common to continents, on the other hand, are often not present on these islands.

In 1703, Alexander Selkrik was part of a plundering group that sailed to the Juan Fernandez archipelago, a few hundred miles off the coast of Chile (pretentiously pronounced “chill-a” by people not from Chile who like to pretend they’re so full of culture). He was voluntarily marooned on one of the islands (Mas a Tierra). He remained there for over four years. He hunted goats and utilized other species introduced by earlier sailors. Little did Selkrik know, his island (now named Alejandro Selkrik Island) was full of these foreign species.

On the island are five species of birds, 126 species of plants, a fur seal, and various insects which are entirely unique to the location. Equally notably, there’s a lot missing from the island. There are no native amphibians, reptiles, or mammals. Islands throughout the world show this same pattern.

Creationism wholly fails to explain the distribution of species – biogeography. It is only in the light of evolution that any logically tenable solution is found. Species are spread across the globe in patterns which follow the movements of the continents. For instance, plants which have a clear common ancestor are explained by the fact that Earth once was composed of a supercontinent known as Gondwana. It split into several sections. This divided species which had already split from one another, causing more adaptation (or extinction). One must believe in tremendous coincidences to just wave this away. That is, the evidence (the biggest foe of the creationist) says plate tectonics caused the movement of the continents which corresponds perfectly to the distribution of species. There is no other plausible explanation.

When observing the world’s biogeography, it is obvious that Australia needs some explanation. Why is it dominated by marsupial mammals while lacking so much in placenta mammals? Better yet, why is the rest of the world lacking in marsupial animals (except for the Virginia opossum)? The answer is in evolution. The animals on Australia show their common ancestry with animals elsewhere by their Class: they are mammals, just as tamarins are mammals. However, they show their divergence and evolution with key differences. Notably, the birthing process and raising of young differs drastically.

Now here’s a prediction that all this makes. Marsupials are found as early as 80 million years ago. Interestingly, they are not found at this time in Australia, but instead North America. With their evolution, they spread to South America about 40 million years ago. About 10 million years later, they’re in Australia. This means there was a connection of land from South America to Australia. The evidence bears this out. Geologists know South America was connected to Antarctica. That in turn was connected to Australia – actually, it was more like a cobble of connection; these continents were all part of Gondwana, deep in the Southern Hemisphere. So, to get from South America to Australia, marsupials must have passed over what is now Antarctica. Prediction: There should be fossils dating between 30 and 40 million years in Antarctica.

It shouldn’t surprise you to learn that, yes, there are marsupial fossils in Antarctica. And yes, they date from 35 to 40 million years in age. Again, a person has to believe in tremendous coincidence to reject this evidence. Geologists independently concluded that Gondwana existed and how it separated, and at roughly what times this all happened. Biologists then concluded that, if evolution is true, marsupial fossils must be presented in a particular location. They were right. Only in the light of evolution does this make sense.

Coyne goes on to explain islands, which I may address in the future. For now, I will leave the evidence at this point. The tremendously short attention span of people – creationists and rationalists alike – forces my hand.

Only in the light of evolution 2

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Only in the light of evolution

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

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

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

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

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

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

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

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

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

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

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

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