Category Archives: Biology

Biblical Absurdities: Is the Bible At Odds With Science?

Introduction

Is the Bible at odds with science? Let us take a look at some of the claims of this book, shall we?

We shall not go in any particular order, but pluck out things as I think of them.

I will not pick on easy things, such as the fact that the Bible asserts that God made the Earth in a few days. Even though we know that the Earth formed over millions of years.

Nor will I focus on the fact that the Earth is not, as the Bible seems to think, a flat circle.

I will not discuss the dome that the Bible asserts is above the Earth which keeps the waters in space from falling onto Earth.

Nor will I go into how Noah could not have gathered two animals of every “kind” onto the Ark.

Nor will I go into the fact that that the Biblical notion of “kind” is completely unscientific nonsense. He did not even have enough room on his Ark!

No, there are many claims the Bible makes about the world or how it works that I will not go into. But what am I going to go into?

I will focus on somewhat less obvious or less well-known ways in which the Bible is wrong.

Bible firmament — So, I guess I will not talk about the dome the Bible claims is over the Earth. But I will show it….

Our List of Blunders

Let us start with what the Bible thinks about insects…

The Bible Thinks Insects Have Four Legs

Here is one of the things the Bible has to say about insects:

All flying insects that walk on all fours are to be detestable to you. There are, however, some winged creatures that walk on all fours that you may eat: those that have jointed legs for hopping on the ground. Of these you may eat any kind of locust, katydid, cricket or grasshopper. But all other winged creatures that have four legs you are to detest.
Leviticus 11:20–23

Insects have six legs, not four. Therefore there are not any four-legged flying insects. Unless the Bible s, for some reason, concerned about insects that have lost two legs.

Surely the Bible authors noticed that insects have six legs?

Well, they noticed they had six limbs. But they did not count two of the limbs as legs. Why? Because at least for the insects described here, they did not consider the two hind legs as walking legs but leaping legs.

But all the same, insects all have six legs. So it is wrong to say that they are four-legged creatures.

The Bible Does Not Know Anything About the Mustard Seed

Let us see which seed the Bible considers to be the smallest seed.

Another parable put he [Jesus] forth unto them, saying, The kingdom of heaven is like to a grain of mustard seed, which a man took, and sowed in his field: Which indeed is the least of all seeds: but when it is grown, it is the greatest among herbs, and becometh a tree, so that the birds of the air come and lodge in the branches thereof.
Matthew 13:31;32

The mustard seed is not the smallest seed. Jesus might not have known that. But I suspect farmers and the like might have known that.

The mustard seed does not grow into a tree either. The mustard plant is clearly not a tree and looks nothing like a tree.

It might have been classified by some as a tree back then because it grew relatively tall. But that is not a scientifically valid reason to classify something as a tree.

The Bible Thinks Pi is 3

Let us turn to the Bible describing a cauldron and see if we can figure out if the all-knowing God knows the correct value of pi.

Also, he made a molten sea [cauldron] of ten cubits from brim to brim, round in compass, and five cubits the height thereof; and a line of thirty cubits did compass it round about.
Kings 7:23-24

The more mathematically astute among you may have already seen the problem. Let me point it out.

Pi is a circle’s circumference divided by its diameter.

The circumference of a circle equals pi times the diameter.

Pi = Circumference divided by diameter.

Now, let us look at what the Bible says. It says that the cauldron is 30 cubits around. So, if we consider the circumference of the circle formed by the rim of the cauldron, it says this circle is 30 cubits around.

It also says that the cauldron is 10 cubits from one brim to the other. So, the diameter of the rim is 10 cubits.

Therefore, according to the Bible:

 Pi = C/d or 30/10 = 3.

But we know that pi is not equal to three. It is about 3.14 and the decimal digits go on indefinitely.

It certainly is not equal to three!

The Bible Thinks the Moon is a Light

Let us see what the Bible says about the Moon, shall we?

And God made the two great lights—the greater light to rule the day and the lesser light to rule the night—and the stars.
Genesis 1:16

This seems to be talking about the Moon. The greater light would be the Sun and the “lesser light” seems to be the Moon.

But there is one big problem with this. The Moon is not a light, it gives off no light of its own. It is a big bunch of rock. People only think it is light because it reflects the light of the Sun.

So the Bible does not even know what the Moon is. Nor that it has no means of giving off any light of its own!

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Biblical Absurdities: Animal “Kinds” – Follow Up.

This is a follow up to this article on the absurdities of Biblical “kinds”. We are presenting some objections to it given on the Metaphysics of Physics Facebook page.

This is a heavily edited version of that exchange where I expand upon the brief arguments I made in the original thread.

I am not going to name the person I am quoting. Here, I am going to call him Antagonist.

What was Antagonist attempting to argue? Essentially, that it is obvious what the Bible meant by the anti-concept of “kinds”. We shall see that is not the case.

Let us get started with his objections.

Isn’t “kind” just another word for “species”?
Antagonist

What gives you that idea? How could it be? The authors of the Bible had no idea of the concept of species as used today.

Until 1686, the term “species” was simply used as a term for a kind of organism. That is, it had little more meaning that used in the Bible.

In 1686, John Ray introduced the biological concept of species as distinguished by always producing members of the same species.

Carolus Linnaeus then formalized the taxonomic rank of species.

So, again, how could the authors of the Bible have the modern concept of species in mind? They did not know about that concept when the Old Testament was compiled over 2,500 years ago!

If it were a known concept back then, why would the Creationists not point this out, instead of refusing to define the term?

They would not talk about their “cat” kinds or “bear” kinds, since “cat” and “bear” kinds are not species.

If by “kind” the Bible meant species, then why does it talk about the “fowl” kind?

Of fowls after their kind, and of cattle after their kind, of every creeping thing of the earth after his kind, two of every sort shall come unto thee, to keep them alive.
Bible, King James, Genesis, 1:25

What is the fowl kind? Who knows what a fowl kind is, whatever the authors of the Bible considered fowls to be?

More importantly, is there a “fowl” species? No there is not. There is no single species that we could logically call a fowl.

Instead, in modern taxonomy, “fowl” is a group consisting of two orders, the Galliformes (gamefowl) and Anseriformes (waterfowl). Each consisting of several species.

So, it seems that the “fowl kind” does not correspond to a “fowl” species.

Let us go into a deep dive of the King James Bible and find every time it mentions kinds.

Keep in mind that later, our Antagonist is going to assert that perhaps the Bible authors meant family or genus. Let us see if we can find any use of the word kind that implies species, family or genus.

And Noah went forth, and his sons, and his wife, and his sons’ wives with him: Every beast, every creeping thing, and every fowl, and whatsoever creepeth upon the earth, after their kinds, went forth out of the ark.
Genesis, 8-18-8:19

Nothing about species, family or genus here. Just vague descriptions of “kinds” which could mean almost anything.

And it shall come to pass, that the fishers shall stand upon it from Engedi even unto Eneglaim; they shall be a place to spread forth nets; their fish shall be according to their kinds, as the fish of the great sea, exceeding many.
Ezekiel, 47:10

Again, nothing about species of family or any genus of fish.

15:39 All flesh is not the same flesh: but there is one kind of flesh of men, another flesh of beasts, another of fishes, and another of birds.
Corinthians, 15:39

Here we are talking about kinds of flesh. It is not clear this is the same … um … kind of kinds. But there are certainly more than one “kind” of best, fish or birds.

In any case, nothing about the concepts of species, family or genus.

For every kind of beasts, and of birds, and of serpents, and of things in the sea, is tamed, and hath been tamed of mankind: But the tongue can no man tame; it is an unruly evil, full of deadly poison.
James, 3:7-3:8

Yet again, no mention of the concept of species, family or genus. What a surprise!

So, how does any of this suggest that by “kind” that the Bible mean species? Or family? Or genus?

Nothing in the Bible indicates this. So, why would we assume this?

Or what we call “family”. Or “genus”. Using a different word for the same concept doesn’t invalidate the concept.
Antagonist

How could it be referring to either the concept of family or genus? Those concepts, as used in modern taxonomy, did not exist back then.

As used today, we can trace the concept to the late 18th century. The first person to use the modern concept of genus was the French biology Joseph Pitton de Tourefort in 1753.

Joseph Pitton de Tourefort, the first person to use the modern concept of “genus”.

So, again, how could the Bible have had these concepts in mind when they were not known to exist then?

So, no this is not a matter of using a different word for the same concept. There is no indication that the Bible is talking about species, family or genus. It gives no indication it is talking about any of these.

Nor did these concepts exist then, as far as we know!

It seems Antagonist is giving the Bible authors credit for taxonomic concepts that were not known to have existed for almost 2,000 years.

I somehow doubt we should attribute a bunch of goat-herders such advanced knowledge.

You say that but give no evidence as to why it couldn’t mean that other than a semantically irrelevant argument.
Antagonist

It is not my place to show that it could not mean that. It is your place to that is what the Bible meant. Which you have failed to do. Which everyone that has ever tried to pin down what the Bible meant has failed to do!

Having said that, I managed to show that what the Bible means is not a species.

Please show me any evidence that the Bible authors meant any such thing.

I’m not saying Creationism is right, I’m saying making a semantical argument and acting incredulous towards a plausible explanation is not an argument.
Antagonist

You have yet to provide me with a plausible explanation. I have pointed out that your “plausible explanations” are not relevant.

You have yet to show that they are plausible explanations for what the Bible meant. Since there is no evidence at all to support that is what was meant.

It is not my place to prove that it does mean that. It is the Creationists place to define what they think the concept of “kind” means. Which they seem unable to do.

Instead, they use the word without giving any definition.

It does not mean species, family or genus. The Bible does not use it in a way consistent with species. Creationists do not use it in a sense consistent with any of these concepts.

Creationists decide things that look or act similar are “the same kind”. And this seems to be how the Bible authors were thinking. But whether they were thinking has nothing to do with “species” or “family” or “genus”.

I’m not saying creationism is right, I’m saying making a semantical argument and acting incredulous towards a plausible explanation is not an argument.
Antagonist

Why are you defending the Bible’s use of the word “kind”? This is a lot like trying to argue with a Creationist. Which is funny because I am reasonable sure that you are not one.

And where is this plausible argument you claim to have presented?

Why don’t they define what they mean by a kind? You would think that if you had a point, you would be able to show this.

You are right though, acting incredulous is not an argument. Good thing I presented arguments then and even better arguments now!

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Biblical Absurdities: Animal “Kinds”.

If you are familiar with the fable of Noah’s Ark, you may recall that the Bible discusses how Noah took two of each kind of animal onto his inadequate Ark. What is all this talk of kinds?

As you would expect, the people that wrote the Old Testament were more than a little lacking when it came to knowledge of taxonomy.

Their knowledge of animals presumably extended to the animals they knew about in their geographic area. As well as, perhaps, some other animals they heard about from those that had travelled to other areas.

They had no way of knowing that there are by some estimates 6.5 million species of land-dwelling animals.

They probably thought that there were only a few hundred, maybe several thousand different species of animals. It seems likely that they had no conception that there might be millions of species of land animals.

So, it is perhaps not surprising that they believed that a giant wooden ark might be able to house two of every species of land animal.

But wait, the Bible does not say species, now does it? No, it does not. It talks of kinds of animals in several places. We will focus on this example of the use of “kinds”:

Of fowls after their kind, and of cattle after their kind, of every creeping thing of the earth after his kind, two of every sort shall come unto thee, to keep them alive.”
Genesis 6:20, King James Version.

What is a kind? Good luck figuring that out. Nobody seems to know. Does that stop the Creationists chiming in? No, of course not.

What do they say a kind is? I do not know what they think a kind is. They do not seem to know themselves.

It would help if we appreciated the problem that they think they are solving. Which is what?

The Creationists seem to be aware that we have a lot of land-dwelling species around us (to say nothing of all the countless extinct ones). So many that two of each of these species could not all have fit onto this mythical boat.

Whoops! But God said two of each kind of animal was on the Ark!

plant kinds — Um, what about all the land-dwelling plants? Did they all get destroyed in the flood? Or did Noah take kinds of plants too?

Yes, two of each kind. Who is to say that kind is the same as the concept of species?

Maybe Noah got two of the cat kind and two of the dog kind and two of the bear kind and two of the rabbit kind and so on.

This seems like it might be helpful. Then Noah does not need nearly 6.5 million species of animals. He just needs two of every kind of animal. And how many kinds of animals are there?

Not nearly as many animals right? Well, this does not really help.

You see, Creationists like to use this anti-concept of “kind” to group all sorts of organisms together into undefined and undefinable groups.

They do this based on grouping together things that look and or act similar. Orwhich they arbitrarily decide are related and hence part of the same “kind”.

For instance, they like to pretend that anything they consider to be a cat, must belong to the cat kind.

Lions look like cats, so they are part of the cat kind. Tigers look like cats, so they too are members of the cat kind.

What about the lynx or panthers? Are they members of the cat kind? Presumably.

But let us consider the Carnivora suborder of Feliformia. This includes the taxonomic order Felidae or cats. I would assume Creationists would classify most or all members of Felidae as the cat kind.

But what about some very cat-like members of Feliformia that are not in the order Felidae and therefore not cats?

What about the extinct family known as Barbourofelidae, a family of sabre-toothed “cats” ? They are not in the Felidae family, but they are closely related to this family.

Are they members of the cat kind?

What about members of the extinct family Nimravidae? These are even more distantly related than the family Barbourofelidae and had different bone structures in the ear to extant Feliformia. As well as more low-slung bodies with shorter legs and tails than typically associated with cats.

Are members of the Nimravidae family considered part of the cat kind?

At what point does something stop being in the cat kind? How dissimilar to cats does something have to be to what they consider cats before it is no longer part of the cat kind?

They do not know! They have no answer to this. Because there is no logical answer to this. There is no clear, logical point where you can logically suddenly decide that something closely related to cats is not part of the cat kind.

We can do the same with any kind they care to name. Such as the bear kind.

Bears are animals of the family Ursidae. But what do Creationists consider to be part of the bear kind? Presumably, brown bears, polar bears and giant pandas and other similar bears, such as the sun bear.

But what about sloth bears? They are members of the family Ursidae, are they part of this bear kind? What about spectacled bears?

What about members of the extinct subfamily of Ursidae known as Hemicyoninae or “dog-bears”? They are very bear-like but also very dog-like. Are they in the bear family or the dog family?

bear-dog kinds — Yeah, is this of the bear or dog kind? How would you know? It looks a lot like both a bear and a dog to me…

Yes, remember we know that bears and dogs are very closely related. Both Ursidae, bears and Canidae, dogs are closely related branches of the family Caniformia.

What kind are the members of the Caniformia family? At what point does something leave this family and become either part of the dog family?

What kinds are members of the Arctoidea family that includes both bears, bear-dogs and mustelids?

Are mustelids part of the bear kind? They are closely related and look a lot like small bears? Or do they form their own arbitrary mustelid kind? Or the Arctoidea kind?

At what point does something stop being a bear and become some related kind?

Creationists have no clear or logical answer. Again, because there is none.

What about rabbits? Rabbits are organisms in the family Leporidae

Are pygmy rabbits part of the rabbit kind? What about the Sumatran striped rabbit which looks quite different? Or the Anami rabbit which barely looks like a rabbit at all? Or the tiny Swamp rabbit which I can hold in my hand?

Are these all part of the rabbit kind?

What about hares? They are rabbit-like. But they belong to a different family, the family Lepus. Are they part of the rabbit kind or a separate hare kind?

What about the Pika? They are another family in the Lagomorpha order which includes rabbits and hares. Are they part of the rabbit or hare kind? Or the Pika kind? Even though they look like short-eared rabbits or hares

What about members of the Glire clade? It is the parent clade of the Lagomorpha order. Where do you draw the line between Glires and members of the Lagomorpha order you consider part of the rabbit kind?

At no point is it clear where something closely related to a cat stops being part of the cat kind. Or where something closely related to a bear stops being part of the bear kind. And so on for every other kind you care to name.

There is never any clear and distinct point where you decide something that is closely related to members of one kind is no longer part of that kind.

It is easy to include things that clearly look like “cats”. But at some point, you have no way to clearly decide which closely related species belong to this kind or another kind. And so on.

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Is “Settled Science” Scientific?

Is there any such thing as settled science? Yes, there is.

But, first, what do I mean by “settled” science? A scientific claim that any rational person would accept as true and established beyond any reasonable doubt. And which they consider will never be replaced by an alternate theory.

You might object that this is not very scientific! We must always keep in mind that we might be wrong. We need to be ready to adjust what we know to accommodate new information that might cast what we know today into doubt!

Yes, that is partially true. We should keep in mind that we are fallible and that we might come to invalid conclusions.

Science, as with any other body of knowledge, is contextual. We study reality and based on what we observe, we form logical conclusions. But we can only account for that which we know about.

For instance, take Newtonian gravity. In the context of not knowing what happens near the speed of light, it was entirely reasonable to accept Newton’s laws of gravity as settled science.

We did not know what happened at extremely high velocities so we had no reason to doubt Newtonian gravity. Newtonian gravity is valid, within the context of things not moving near the speed of light.

Then, we expanded our context to be able to account for things near light speed. We realized that in that context, Einstein’s relativity provides better mathematics for what happens with gravity at near light speed.

Does that mean that we had no reason to be certain about Newtonian gravity?

No, it does not. We knew that it was an extremely accurate description of gravity at speeds much lower than the speed of light.

That is why NASA uses Newtonian gravity for most purposes, even though relativistic equations would be more accurate. Newtonian gravity is easier to deal with and is extremely accurate at the speeds NASA tends to work with.

You may have noticed rockets do not go at anything near the speed of light. So, Newton’s gravity equations will work just fine thanks.

Certainty is contextual. Suppose in the context of our knowledge, the available evidence supports a theory. We are therefore entitled to some certainty about that theory.

But what if it turns out that we are wrong? After all, we used to believe some strange things.

We used to think things burned because of phlogiston. Phlogiston was a mysterious substance that was thought to exist in all combustible bodies.

We used to think that dinosaurs were all sluggish, scaly critters that probably lived in swamps to support their massive weight.

Well, yes. Sometimes we are wrong. Our theories are sometimes not supported by facts. We have no business accepting some theories as anything more than a plausible hypothesis.

These are the theories which do not make up the body of settled science. These are the theories we should not consider settled.

However, it would be dishonest to consider a theory settled in the absence of evidence. It would also be dishonest to consider a theory settled if we did not understand it well enough to be sure it was consistent with all the available evidence.

Having said that, some theories are entirely reasonable within the context of the available evidence. Sometimes all the known evidence points to these theories being true.

Sometimes we understand the theory well enough to reasonably conclude it is entirely consistent with the facts. Therefore, we can be certain about these theories.

We should not entertain serious doubt of theories that have substantial evidence behind them.

We can always imagine that some theories might be disproven. However, we should be certain about a theory if all the available evidence points to it being true.

Certainty does not require us to magically account for the possibility of a context of knowledge we do not currently possess. We can be certain that something is true even if there is something we do not know about now that may later show that it is not true.

Certainty is contextual, it is valid to be certain based on the context of available evidence. As long as we are willing to address any evidence that arises should the context of our knowledge change.

In other words, we can be certain something is true. And yet adjust our theories when the context of our knowledge expands.

However, there are theories that we can consider completely and forever settled. These are theories we know with certainty and can prove without any shadow of a doubt to be true.

We know these will never be shown to be false.

It would contradict known facts of reality if they were not true. Things would have to not be what we know that they are.

Examples of these would be that atoms exist. We know atoms exist; we have seen them. If they did not exist, almost everything we know about chemistry and atomic physics would not be true.

We know evolution happens. We might not know everything about how it happens, but we know that it does. To disprove evolution, we would have to invalidate almost everything we know about biology and the known facts of biology would have to be other than what they are.

We know that the Earth is round and that it orbits the Sun. To invalidate this, the direct evidence of our senses would have to be wrong! The fact that we can see that the Earth is round would have to be fake. And how would we explain the observed behaviour of Earth if it does not orbit the Sun?

Yes, because it is much more scientific to think this might be real, right?

We can say without a shadow of a doubt that theories like this are absolutely and forever settled and that we will never find anything that contradicts them. We know that no such evidence is even possible.

Such science is completely settled. It would be nonsensical to pretend otherwise!

So yes, there is such a thing as settled science. It is baseless to pretend otherwise. And it would be intellectually dishonest and non-scientific to pretend that it is not settled!

It is unscientific to question that the Earth might not be round. Or that evolution does not happen. Or that atoms do not exist. Why?

Because we have seen that the Earth is round! Are we to question the evidence of our senses so that we can become a Flattard?

It would contradict the obvious implications of the evidence of our senses to believe atoms do not exist. Additionally, we have seen atoms!

It would go against observable facts and their logical implications to question that evolution happens.

It would be unscientific to question that light exhibits wave behaviour. This would go against the evidence of our senses and the logical implications of that evidence.

To question theories which we can show are irrefutable facts based on the evidence of our senses and the logical implications of such, is unscientific.

Your belief that the irrefutable facts of reality might be wrong is completely nonsensical and unscientific.

The ability to entertain alternatives to the way reality works is not indicative of science, it is closer to the mindset of the religious person that must evade reality to maintain the possibility of his delusions.

The questioning of everything, even things we can prove beyond any reasonable doubt is little better than those that deny science outright.

To deny the absolute certainty of that which we can show beyond any reasonable doubt, is to either partially deny the veracity of the evidence or fail to understand that science is about the study of an objective reality, not blind guesswork.

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Phylogeny Tracker: Clades Animalia to Thelodonti

In this series, we trace interesting phylogenetic relationships between clades of organisms. This is mostly a fun exercise in taxonomy, but it also helps demystify the complex relationships between various groups of organisms.

Today we are looking at the path that leads from Animalia, all the way to Thelodonti.

Follow along by using the Phylogeny Explorer. Click along the indicated links in the tree so you can eventually get to Animalia.

Note that the Phylogeny Explorer refers to this clade as the Anapsid-Thelodont clade. We will continue to refer to this as Thelodonti.

What is the Thelodonti clade? It includes all jawless fish with distinct scales instead of armour. The homo clade branches off this one. But with many, many subbranches between them.

We start with the Metazoa or Animalia clade, as we agreed we would. Only the most stupid person would deny that fish are all animals!

We must now head down the Eumetazoa clade. This includes all animals more advanced than sponges. It is safe to say that fish are more advanced than sponges. So, down the Eumetazoa branch we go!

Now, fish have bilateral symmetry as an embryo. That is, their left and right sides are mirror images of each other. This means that they also have head and tail as well as a belly and a back. This makes them members of the Bilateria clade.

Note that not all Bilateria maintain their bilateral symmetry as adults. Bilateria are bilateral symmetrically as embryos but might be as adults. For instance, the echinoderms are bilaterally symmetrical in the embryonic stage. But as adults, they achieve pentaradial symmetry instead of bilateral symmetry.

clades — There are lots of interesting symmetries in biology. Bilateral symmetry was a big one!
**“Diagram comparing bilateral, radial, and spherical symmetry” by Charl Hutchingsis licensed under CC BY 4.0.**

So, down the Bilateria branch we go!

Fish are deuterostomes, so as this includes deuterostomes, we must head down the Nephrozoa branch next.

During embryonic development of fish, the first opening, the blastopore, becomes the anus. Every fish is at some point nothing but an … well yes.

Anyway … this makes fish a deuterostome!

Next, we must head down the Chordate branch. This clade is defined as all organisms with the following at some stage of their life-cycle/during embryonic development:

A flexible rod formed of a material similar to cartilage called the notochord. In vertebrates, such as fish, this later develops into the spine.

The presence of a hollow nerve cord dorsal to the notochord, known as a dorsal nerve chord. In vertebrates, such as fish, this develops into the spinal cord.

The presence of pharyngeal slits. In the case of fish, these develop into gill arches, the bony or cartilaginous gill supports.

The presence of an endostyle. This is an organ that assists in filter-feeding and seems to suggest that the common ancestor of chordates was a filter-feeding organism.

The presence of a post-anal tail at some point in their embryonic development. Of course, unlike humans, fish maintain this feature in the form of their visible tail!

They are also bilaterally symmetric, possess a coelom, metameric segmentation and a circulatory system.

So, we have gone down the Chordate branch, where next?

Fish, as with most chordates, have an olfactory nerve, so down the Olfactore clade we head.

Fish have well-defined heads so down the Craniata branch we head. This branch includes all organisms with well-defined heads with brains, sense organs, eyes and a skull.

Now, our fish have a backbone, so we go down the Vertebrata branch.

Yes, we just saw that apparently the olfactory nerve predates the development of distinct heads and backbones! The sense of smell predates skulls and backbones. Neat!

Next, we head down the Agnatha-Pteraspidomorphi branch. These are believed to be a parent clade which is possibly ancestral to all jawed vertebrates. And ancestral to Thelodonti.

Since fish have a dermal bone, we head down the Pteraspid-Anapsid branch.

And now we find the Anapsid-Theolodont branch. These are the jawless fish with distinct scales instead of armour and what we were looking for! Finally!

That took a while! But we got there in the end and took a good look at some of the most basal groups of animals.

What phylogenetic journey will we go on next time? I have not decided yet, but I am sure it will be interesting!

Stay tuned!

Phylogeny Tracker: Clades from Biota to Animalia

In this series we trace interesting phylogenetic relationships between clades of organisms. This is mostly a fun exercise in taxonomy, but it also helps demystify the complex relationships between various groups of organisms.

Today we are looking at the path that leads from Biota, the root of life, all the way to animals.

Follow along by using the Phylogeny Explorer. Click along the indicated links in the tree so you can eventually get to Animalia.

We first have to take the Eukaryota clade. All animals consist of multiple cells with a nucleus, so they are eukaryotes.

Animals cells have either one or no flagellum, so they are unikonts. Animals also have a triple-gene fusion only in Unikonta. So therefore, we must now turn down the Unikonta clade.

Next we turn down the Obazoa clade. Not much is known about this understudied clade, but it includes animal and fungi, so down this clade we must go.

The flagellate cells of animals, such as sperm, propel themselves with a single posterior flagellum. This is a common characteristic of the Opisthokont clade. Fungi are in this clade, but some have lost their flagellum.

Next we must go down the Holozoa clade. This includes all animals and their most closely related unicellular sisters (e.g. choanoflagellates). But not fungi. Most unicellular holozoans are parasites.

Animals cells maintain the slender thread-like projections or “tentacles” of the ancestral Opsithokont cell, so now we must head down the Filozoa clade.

Both animals and choanoflagellates are able to form multicellular units. Animals are permanently multicellular, while choanoflagellates can form multicellular colonies. So now we head down the Apoikozoa (“Colony Animals) clade.

Finally we reach Metazoa, or Animalia. What are the characteristics of animals? Many. We will cover over some of the more readily grasped ones.

They are eukaryotic and multicellular. Unlike plants and algae, which produce their own nutrients, animals are heterotrophic, that is they cannot produce their own food and must ingest it from an external source.

With few exceptions, they respire aerobically. That is they require oxygen in order for cells to produce oxygen.

All animals are motile at some stage of their life-cycle, including the sponge. That is, at some stage of their life cycle, they are mobile. Although, later in life they may become sessile (unable to move by their own power).

Alright, that will do for our brief coverage of the key characteristics of animals. We have seen that to get to Animalia, we have to pass through several basic clades.

Next time we will start off in the Animalia clade and see how long it takes to get to Thelodonti, that is a clade of jawless “fish” with distinct scales, rather than large armor plates. We will have to pass through more than ten clades to reach this point.

It will take us a few just to get to Chordata (animals with a notochord), which include the vertebrates!

Stay tuned.

The Primitive Non-Argument Against Reality, Part Two

Today we are going to continue defending reality by looking at this article, “The Evolutionary Argument Against Reality”. You can find part one here.

Last time it was alleged that we do not see reality as it is and that a better perception of reality is not a survival advantage.

We debunked that nonsense easily. What nonsense can we debunk today? Let’s see.

Hoffman is, naturally enough, asked how seeing a false reality can be beneficial to an organism’s survival.

He then precedes to give us the analogy of what we see on the screen of our desktop computer.

We see icons on our screen. These icons represent all kinds of files. Say you look at one of the icons on the lower right and it looks like a blue rectangle and if you click on it you get a Word document.

Does this mean that the Word document is blue and a rectangle and lives in the lower right of your computer? Of course not.

That blue rectangular icon guides my behaviour, and it hides a complex reality that I don’t need to know. That’s the key idea. Evolution has shaped us with perceptions that allow us to survive. They guide adaptive behaviours. But part of that involves hiding from us the stuff we don’t need to know. And that’s pretty much all of reality, whatever reality might be. If you had to spend all that time figuring it out, the tiger would eat you.

The icon is indeed an abstract representation of something. It represents a file.

What is a computer file? Does the file itself physically exist on the computer? If so, in what form?

I would argue that no, the file does not physically exist on the computer. What exists is a bunch of electrically charged segments of your storage devices (hard drives, memory and so on). The charge of those segments is read and show on your screen in a certain pattern.

Is this a real thing in your computer? Well, obviously not…

We have an abstraction for that pattern of charges, which we call a “file”. A file or a program refers to a bunch of charged matter and those relationships between the charges is what we call a “file” or a “program” or some section of either.

So, the file is itself an abstraction. The icon we click on to access the file is also an abstraction. It is an abstract way of referencing the file.

But what are we clicking on? When we “click on the icon”, we are moving our mouse and instructing our computer to open that file.

When we “click on an icon” we are engaging in a process which results in our file being read. Which is to say, the process causes those bits of charged matter to be read.

Virtually everything we do with our computer involves many, many abstractions.

What physically exists is a bunch of charged particles. From this, we form the abstraction of “files” to refer to collections of charged particles.

But we need still further abstractions to be able to do things efficiently with our computer. We must form abstractions like “folders” and “desktops” so that we can efficiently deal with abstractions such as “file”.

These abstractions are presented to us in the form of the icons and other visual elements. The icons do not physically exist qua icons. They exist as flashes of light on the screen. But we interpret certain patterns of lights as representations of things such as icons.

Does that mean that when we see the icon, we are not seeing things as they are?

No, it does not.

The icon is not some false perception.

It is an abstraction that allows us to deal with other abstractions such as files.

The icon hides details from us that we do not need to know. It allows us to deal with files without having to find out where on the disk a file is located. Or even which folder on your computer it might be on.

And of course, the folder is itself another abstraction that hides details from us.

But all that means is that when using a computer, we use a lot of abstractions which help us avoid having to deal with a lot of details that we do not need to know about.

It is not an argument against the validity of the senses, for not seeing things as they are as an advantage.

It is an argument for the importance of increasingly higher-level abstractions. Without which it would be very difficult to efficiently do much of what we currently do with our computers.

It’s an application of the epistemological concept called unit-economy.

Ayn Rand has more to say about abstractions and unit-economy.

But we won’t go in much more depth about that here. You can find out more about unit-economy here.

Hoffman is then asked if everything that we see is one big illusion.

We’ve been shaped to have perceptions that keep us alive, so we have to take them seriously. If I see something that I think of as a snake, I don’t pick it up. If I see a train, I don’t step in front of it. I’ve evolved these symbols to keep me alive, so I have to take them seriously. But it’s a logical flaw to think that if we have to take it seriously, we also have to take it literally.

Why should we not take what we see literally? We argued in part one of this series that the senses are valid and do not distort things. We have no reason not to take them literally.

So, Hoffman is then asked if snakes are not snakes and trains are not trains, what are they? A logical enough question.

Snakes and trains, like the particles of physics, have no objective, observer-independent features. The snake I see is a description created by my sensory system to inform me of the fitness consequences of my actions.

Your sensory system gives you sensations from which you can make out objects. One of which is an object which is subsumed under the concept of “snake”.

Your senses give you nothing but sensory data. They just collect data.

It is up to your mind to form abstractions such as “snake” which describe concrete entities subsumed under those abstractions.

Your senses do not know anything about the concept of a snake. It is not able to create some illusion of a snake based on what it thinks a snake is. Your senses feed your brain data and your brain identifies things like a “snake” based on that input.

Any error in identification is not the fault of your senses. It is the fault of your mind for failing to form proper abstractions.

You cannot blame your senses for such mistakes.

Unless, of course, your senses are compromised with medical conditions, old age and the like.

As for snakes and trains and the like having no objective, observer-independent features, that is nonsense. To exist at all is to have objective features. That is part of what it means to exist.

My snakes and trains are my mental representations; your snakes and trains are your mental representations.

We observe the same things. Which we may or may not classify as snakes and trains, depending on how we form these abstractions. Nonetheless, we are observing the same reality.

Hoffman seems to genuinely be trying to argue that “Reality is complicated and it is good that we do not see things as they are. If we did, reality would be too complicated to deal with”.

It is true that every organism only has a certain range of forms of perception. There are countless forms of sensory organs known to exist and no animal has them all. There are only so many ways they perceive things.

But whatever they do perceive is reality as it is. It might, for some organisms, be only a relatively limited window on reality, using primitive sensory organs, but even then, they are seeing what is.

Even if what they sense is part of the whole, they are still sensing what exists objectively in reality.

The senses cannot give us what is not. That is not how they work, as we argued in part one.

Even then, it is hard to see that a distorted perception of reality could be an advantage.

The fact that there are things we do not perceive is not an argument for our senses deceiving us. Our senses do have a limited range. But the fact that they are not omniscient does not mean that they are wrong.

That will do for this part. We will return to this article in the future and see what other insanity Hoffman can “offer” us.

The Primitive Non-Argument Against Reality, Part One

Today we are looking at this article, “The Evolutionary Argument Against Reality”.

In the words of the article:

The cognitive scientist Donald Hoffman uses evolutionary game theory to show that our perceptions of an independent reality must be illusions.

We shall see this is impossible. This is a gross misuse of mathematics. And is based on distorted view of natural selection.

We will get started with the first paragraph of the article.

As we go about our daily lives, we tend to assume that our perceptions — sights, sounds, textures, tastes — are an accurate portrayal of the real world.

We do not need to “assume” that. Our sensory organs passively perceive reality as it is. They have no means of distorting reality and showing us things as they are not.

Our visual cortex and other parts of our brain process the input of the senses. But they do not distort that input. They simply present the input of our senses to our consciousness. They do not fabricate or distort their inputs.

Everything we experience is an accurate portrayal of the real world, according to our mode of perception. There are different modes of perception. But that does not mean our senses are subjective or that we do not see reality as it is.

For example, we see things in color. Other organisms do not. Does that mean the senses of those organisms are invalid? Or that they do not see reality as it is?

No. It simply means that those other organisms have a different mode of perception. They observe the same facts of reality. But their senses present those facts differently.

Different modes of perception are not an argument for the subjectivity of those modes of perception. They simply mean that different organisms perceive the same facts of reality in different ways.

Do black and white photos invalidate our senses? No more than the fact that some organisms do not see color. Which is to say, not at all.

Nor does it prove that there is any distortion occurring. Different modes of perception are not kinds of sensory distortion.

Sure, when we stop and think about it — or when we find ourselves fooled by a perceptual illusion — we realize with a jolt that what we perceive is never the world directly, but rather our brain’s best guess at what that world is like, a kind of internal simulation of an external reality.

No. Our senses are not some kind of distorting lens that gives us a false view of reality.

Nor is what we perceive “our brain’s best guess at what the world is like”. It is an accurate representation of reality according to our mode of perception.

Indeed, we do not perceive everything that exists. We only perceive those things that are detectable by our senses. We will return to this a little later.

Episode sixteen of the podcast covers the topic of optical illusions.

In short, optical illusions are not an argument against the validity of the senses. When we observe an optical illusion, our senses are giving us valid data.

Neither our senses nor our brains are distorting the data. We are seeing things as they are. When we see bent straws in water, that is not our senses tricking us. That is how we observe light rays bent by water.

But if we want to better understand what we are observing, we must think and “see past” the illusion. We must understand that we need to process what we are seeing, which is real.

We need to more closely understand how it is consistent with reality. And then abstract away that optical illusion so that we can understand things better.

This does not invalidate our senses either.

The world presented to us by our perceptions is nothing like reality. What’s more, he says, we have evolution itself to thank for this magnificent illusion, as it maximizes evolutionary fitness by driving truth to extinction.

This obviously cannot be true. As we have seen, there is no false dichotomy between the world as we see it and as it is. We see what is. There is no alternative. We cannot see things as they are not.

Furthermore, evolution could not make any of this true. Evolution is a process whereby the gene pools of populations change. According to changes in the environment and other factors.

Living organisms undergo countless genetic changes in every generation. You have several such genetic mutations. Although most of them do not impact your life in any noticeable way.

Those mutations that are harmful to the survival of an organism tend to be less likely to be passed down to future generations. Survival can be tough enough as it is. Those with a genetic disadvantage are less likely to survive to have offspring.

Natural selection is the process by which genetic changes that are beneficial to survival tend to be passed on. It favors those changes which help increase the chances of survival. While tending to weed out many of the changes that would negatively impact survival chances.

Suppose an organism was less able to perceive the world as it is. That would make it harder for that organism to deal with reality. And thus, seriously impact its chances of survival.

Such unfortunate specimens are very unlikely to have offspring. Let alone offspring that survive to have offspring.

There is no way that being unable to see reality as it is could maximize evolutionary fitness. Only those with the greatest chances of survival maximize their evolutionary fitness. Not those with pathetic to zero chances of survival.

As for evolution driving truth to extinction, that is utter nonsense. The truth is what the facts are.

Natural selection is an extremely brutal and merciless process. Those changes which objectively enhance an organism’s chances of survival are likely to be passed on.

Those which are not in line with the brutal reality of nature tend not to be passed on. Life in the wild is hard and those changes which are not in accordance with the objective needs of the organism are less likely to be passed on.

In a sense, this makes natural selection and evolution itself, heavily subservient to the truth. To the objective requirements of an organism’s survival. Not something which somehow obliterates truth.

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Episode Twenty Five – Fragment and Pandemonium Interview with Warren Fahy (No Spoilers)

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Today we have an interview with Warren Fahy, author of the books Fragment and Pandemonium. We are going to talk about these books as well as about some biology stuff. Should be fun!

Some of you may not know what these books are. Well, Warren is going to tell us all about them in a little bit. But they are science thrillers something along the lines of Jurassic Park.

You can probably gather by the fact that I am interviewing him about these books, that I have read them and probably enjoy them.

Yes, I have read them and I do enjoy them. Fragment and the sequel are amazingly interesting books with some extremely compelling biological theories.

There are some truly terrifying, nightmare creatures in both of them. They make the dinosaurs and monsters in other books seem tame. Dragons? T-Rexes? The critters in these books, such as spigers are much deadlier and scarier.

I also quite like the main cast of characters, but I cannot talk about that very much without spoilers. But two of them are biologists and they may or may not have some fascinating biological ideas, new and old.

Highly recommended. But more than that and as entertaining as the scary monsters are, you might also learn something reading this.

You can find out more about and buy both of these books here:

This is the non-spoiler version of this episode. If you have read these books, you might want to go to the other version of the podcast here. It has a lot of the same stuff, but without spoiler content removed.

Please note that we cannot be 100% sure that there is not some spoiler we missed in here. It might be best to read the books before listening to this podcast!

We have not presented the transcript of this in web page form. Instead, you can listen to the audio or download the PDF transcript.

However, there may be mistakes in the transcript. Any mistakes in transcription represent our own errors or a transcription error we missed.

Click here to download the PDF transcript.

Episode Twenty Five – Fragment and Pandemonium Interview with Warren Fahy

Podcast: Play in new window | Download

Today we have an interview with Warren Fahy, author of the books Fragment and Pandemonium. We are going to talk about these books as well as about some biology stuff. Should be fun!

Some of you may not know what these books are. Well, Warren is going to tell us all about them in a little bit. But they are science thrillers something along the lines of Jurassic Park.

You can probably gather by the fact that I am interviewing him about these books, that I have read them and probably enjoy them.

Yes, I have read them and I do enjoy them. Fragment and the sequel are amazingly interesting books with some extremely compelling biological theories.

Highly recommended. But more than that and as entertaining as the scary monsters are, you might also learn something reading this.

You can find out more about and buy both of these books here:

If you have not read these books, you might want to go to the non-spoiler version of the podcast here. It has a lot of the same stuff, but with some spoiler content removed.

Please note that we cannot be 100% sure that there is not some spoiler we missed. It might be best to read the books before listening to this podcast!

We have not presented the transcript of this in web page form. Instead, you can listen to the audio or download the PDF transcript.

However, there may be mistakes in the transcript. Any mistakes in transcription represent our own errors or a transcription error we missed.

Click here to download the PDF transcript.