Introduction

Evolution has let some traces in living beings. They are called palimpsests, from Ancient Greek παλίμψηστος, litterally "scraped again". They are relics of former properties of a species. They are mainly traits that blurred with time (i.e. with evolution): they haven't completely vanished, as we can notice in different ways; they are remnants. We distinguish vestiges, atavisms, bad design, dead genes, and palimpsests in embryos. All these remnants (the Latin origin of the word, remanere, "stay", describes it well) are undeniable evidence for evolution.

Vestiges

What are vestiges ?

Vestiges are degenerated or imperfectly developed organs or structures that have little or no utility, but that in an earlier stage of the individual or in preceding evolutionary forms of the organism performed a useful function.

What does the evolutionary theory say about vestiges ?

The opponents of evolution say that a trait can't be vestigial if it still has a function , or a function yet to be found. But in fact they missed the point. The evolutionary theory doesn't say that vestigial characteristics have no function. A trait can be vestigial and functional at the same time. It's vestigial because it no longer performs the function for which it evolved, and not because it's functionless.

Some examples:

Flightless birds

The wings of ostriches are good examples of vestiges. Like all flightless birds, ostriches are descended from flying ancestors and we know it from both fossil evidence and from the pattern of ancestry that flightless birds carry in their DNA , but they actually can't fly despite the fact that they still use their wings. Yet the wings are not useless, they've evolved new functions. They help the ostrich to maintain balance, mate , and threaten its enemies. We say then that the wings of ostriches are a vestigial trait : a feature of a species that was a useful in its ancestors, but that has lost partially or completely its usefulness , as in the ostrich , has evolved for new uses.

There are many other different flightless organisms as for examples the New Zealand kiwi , the kakapos , the ducks , and of course the penguins. The wings of some of these species evolved new functions as for example the penguin , which ancestral wings have evolved into flippers , allowing the bird to swim underwater with amazing speed. But in some , like the kiwi , the wings are so small that they don't seem to have any function. They're just remnants.

Why did some species lose their ability to fly ?

The scientists are not absolutely sure, but they have some ideas. Most of the birds that evolved flightlessness live on islands - the extinct dodo on Mauritius , the Hawaiian rail, the kakapo and kiwi in Zealand , and the many other flightless birds named after the island they inhabit. As we'll see in the chapter " The geograpahy of life " , one of the notable features of isolated islands is the small amount of mammals and reptiles - species that are dangerous predators for birds. The species that live on continents and not on islands , as ostriches , all evolved in the Southern Hemisphere, where there were far fewer mammalian predators than in the north.

Let's say it easier : flight is metabolically expensive , using a lot of energy that could otherwise be diverted to reproduction. Birds mainly fly to stay away from predators , but on islands predators are often missing and food is obtained on the ground, so there is actually no real need for fully functioning wings.

See appendix 1

Vestigial eyes

Vestigial eyes are also common. Many animals, including the burrowers and cave dwellers, live in complete darkness, but the scientists know from evolutionary trees that they descended from species that used to live aboveground and to have functioning eyes. It means that like the wings the eyes use energy, and they can easily be injured. For these reasons, mutations that favour their loss would be advantageous when it's just too dark to see. Alternatively, mutations that reduce vision could simply accumulate over time if they don't help and hurt the animal.

Such an evolutionary loss of eyes occurred in the ancestor of the eastern Mediterranean blind mole rat. This is a long, cylindrical rodent with a tiny mouth.This animal spends its entire life underground.But despite this fact, it still has a vestige of an eye – a tiny organ only one millimeter across and completely hidden under a protective layer of skin. This eye can't form images. Molecular evidence tells that, around 25 million years ago, blind mole rats evolved from sighted rodents, and their vestigial eyes attest to this ancestry.

But why don't these vestigial eyes in the blind mole rats completely disappear ?

Recent studies show that they contain a photopigment that is sensitive to low levels of light, and helps regulate the animal's daily rhythm of activity. This function driven by small amounts of light that penetrate underground, could explain the persistence of vestigial eyes.

And what about the vestigial eyes in the other species ?

True moles, which are not rodents but insectivores, have independently lost their eyes, keeping only a vestigial, skin-covered organ that you can see by pushing on its head. Similarly, in some snakes , the eyes are completely hidden under the scales. Many cave animals also have eyes that are reduced or missing. These include fish ( like the sightless cave fish you can buy at pet stores ) , spiders , salamanders, and so on. There is even a sightless cave crayfish that still has eyestalks, like the snails , but no eyes on top of them.

See appendix 2

Vestigial pelvis

The vestigial pelvis is also one example of vestiges. In fact many living species, as whales, have a vestigial pelvis and leg bones, testifying to their descent from four-legged terrestrial ancestors. If you look at a complete whale skeleton in a museum , you'll generally see pelvis bones hanging from the rest of the skeleton. That's because in living whales, these pelvic bones are disconnected to the rest of the bones, but are simply implanted in tissue.

Human's appendix

The appendix is the most famous of our human vestigial features proving that we evolved. The appendix is a thin, pencil-sized cylinder of tissue that forms the end of the pouch that sits at the junction of our large and small intestines. Like many vestigial features, its size and degree of development are highly variable: in human, its length goes from about an inch (= 2.54 cm) to over a foot (= 30.48 cm).A few people are even born without one. Our appendix is simply the vestige of an organ that was extremely important to our leaf-eating ancestors, but that has no real value to us , as we don't eat leaves now and can't digest cellulose, the appendix is nearly gone.

See appendix 3

Human's coccyx

We, humans, have other vestiges of primate ancestry. We have a vestigial coccyx. It's the triangular end of our vertebral column.It's what remains of the long and useful tail of our ancestors. The coccyx has now lost its original function in assisting balance and mobility, but it still serves some secondary functions,as being an attachment point for muscles. It's the reason which explains why it didn't disappear completely. Remember: it's vestigial because it no longer performs the function it originally had and not because it's usefulness.

See appendix 4

Atavisms

What are atavisms?

Atavisms are currently disappeared features of the former species that reappear.They don't appear regularly but are occasionally present in individuals. These features were once useful, but silenced when they lost their utility (see below). This is the main difference with vestiges: vestiges are reduced traits, whereas atavisms are resurgences of complete traits.

An example to distinguish atavisms from vestiges:

The ancestor of humans had a tail. In normal humans, the only trace left is the coccyx (last vertebrae): we all agree it is not a tail. It is a vestige, a "diminished trait". Rarely, some individuals are born with true tails: in this case, we speak of atavisms since the trait reappears in force and magnificence.

See appendix 5

Why aren't atavisms recurrent in a species?

Atavisms are due to the sporadic reactivation of genes that are no longer needed by the species and have thus gradually disappeared because of natural selection.

What is natural selection?

It is the process during which, in a given environment, favoured species survive and unfavoured ones die. The survivors reproduce much more and transmit their genome to their offspring. Because of the environment in which a species evolves, some traits show more useful than others: useful to survive from predators, to find food, or more efficient regarding energy loss.(1) In this case, we say the individual presenting these traits are favoured.

Do traits only disappear?

No. Even if some traits appear, others disappear; it all depends on the trait, case by case. However, only disappeared traits are important for atavisms, since they are reappearances.

How is it then possible that some traits appear again?

If the phenotype (the appearance) doesn't show a certain trait, it is still there in the genotype (the information); the genes related to the trait were deactivated: they "sleep" but don't disappear completely. Rarely, such genes "wake up", and an atavism is generated.

What are genes?

Genes are the carriers of the informations that compose us. In the nucleus of each cell, there is DNA,a long string on double-helix structure, divided into chromosomes. In human DNA, there are 23 pairs of chromosomes. The fact that they come in pairs will be important later on. DNA is made of a very big amount of four types of molecules, which assemble one after another in a specific order. These four molecules are taken by triplets, and each triplet has its corresponding protein. (If the molecules are the plan, the proteins are the material of a building.) If we summarize: DNA is made of chromosomes, which are made of genes which are made of a string of four types of molecules. DNA carries absolutely all the information about our body structure and functioning.

How are traits transmitted?

Remember: each cell of each human being has, unless there is an abnormality (not enough or too many chromosomes), 23 pairs of chromosomes. In each pair, there is one maternal half, one paternal half. Although the two components of a pair are not exactly identical, their structures resemble: the same structure of genes is found in each. Very often, however, only one gene, either maternal or paternal, is called dominant, which means that it is the one that determines the phenotype (appearance) of the individual. If the gene U determines the shape of the earlobes, and the paternal half is Ŭ, the maternal one, Ū, and if Ŭ is dominant, the individual will have "its father's ears", but in the genotype (the non-appearing characteristics of a trait, contained in the genome), its ears are ŬŪ. It might transmit his Ū gene to its offspring. If, for any reason, Ū is more favourable for the species, individuals having Ū ears will tend to survive more, thus reproducing more, thus transmitting the Ū characteristics to the descendants.

(1): http://www.biology-online.org/dictionary/Natural_selection

Dead Genes

What are dead genes ?

A dead gene is a gene which doesn't function. It is also called a pseudogene. Dead genes are the consequence of a trait, which becomes reduced or useless, like atavisms and vestigial traits. The genes that produce it stay in the genome, despite the fact they stop their action, in other terms their function. Normal function of a gene is to make a protein —a protein whose sequence of amino acids is determined by the sequence of nucleotide bases that make up the DNA. However if the DNA sequence of a given gene is expressed abnormally, it makes a non-functional protein. So we call it "dead" gene.

Some examples :

The GLO pseudogene

The GLO gene codes for an enzyme which is used to make vitamin C. Vitamin C is essential for proper metabolism and the pathway to make it is vitually present all mammals, except for primates, fruit bats and guinea pigs. In these species vitamin C is obtained directly in their diet and normal diets have enough of this molecule. Primates as guinea pigs and fruit bats don't need to synthesized the vitamin C because they don't need to do so. However, they do carry the genetic information to make the vitamin.

In those species, the last step of the pathway, requiring the GLO enzyme, allowing vitamin C to be synthesized is blocked. GLO has been inactived by a mutation: the gene is not functional any more but still present: that's why it's called a pseudogene. Mutations have modified or removed some nucleotides in the gene, that is why they have destroyed the ability to make vitamin C in these particular species. Interestingly, this pseudogene has not been completely lost in the process of Evolution but it is transmitted from generation to generation.

Endogenous retroviruses

"Endogenous retroviruses" belong to the dead genes. This means that some species also carry some dead genes that came from other species, namely viruses. However when those species are infected, these dead genes can make copies of their genome and infiltrate themselves into the DNA of the infected individual. If the viruses damaged the cells that produce sperm and eggs, they can be passed on to the descendants.

Fortunately, most of them became harmless thanks to mutations. That is why they are the remnants of ancient infections.

The sense of smell

Humans can still recognize more than ten thousand different odours. However they are considered as bad sniffers among land mammals. In our DNA we have many olfactory receptor (OR)genes. These genes allow us to differentiate odours.

Why is smell so useful and essential for some species ?

For some species, their sense of smell is essential, because their vision is much less developed than smell. They need to have a good sense of smell especially to find a mate, to locate food, to recognize predators and to see who's been invading their territory.

How has natural selection tapped them?

With time and many duplications of the ancestral gene, an accident during cell division appeared. Gradually, the duplicated copies diverged from each other and with each gene's products binding to a different odor molecule. For each of the thousand OR genes there is a different type of cell which has evolved. The brain also evolved to rewired and combined the signals from the diverse kinds of cells to different odors.

Why are humans bad sniffers?

For humans and primates the vision is more important than smell. Among the total of eight hundred OR genes in humans and primates, alsmost the majority are pseudogenes, permanently inactivated by mutations. Despite of the useless genes, humans and primates still carry this total of eight hundred OR genes.

Why are "dead genes" still present despite of their uselessness?

In the past, dead genes were actived und usefull. However, with time and some mutations or in other terms thanks evolution, these genes which were useful in the past have lost their primary function and became pseudogenes or dead genes. So that is why they are now useless.

Then ancestor genes were transmitted to offspring and these dead genes don't disappear. Anything destroyed these dead genes, that is why thanks to transmition to the next generations dead genes are still present despite of their uselessness.

Palimpsests in embryos

Scientists noticed that the embryos of all vertebrates start developing in the same way; depending on the species, their later development diverges following quite a precise process.

What is the developmental process of an unknown embryo?

All embryos start developing in the same way: like fish. Already then, their development differs form the other ones' according to their class. Fish embryos develop into... fish, and their specific characteristics, according to the species they belong to. Amphibians develop as follows: the fish-like embryos continue developing, changing their shape, organs, etc. into the ones of amphibians. Reptiles develop as follows: fish-like embryos, amphibian-like embryos, reptiles. Mammals develop from reptile-like embryos (obtained by the same sequence as preceding) into mammal-like ones. A German evolutionist from the 19th century, E. Haeckel, said the embryo at an early stage looks like the adult of the class corresponding to the stage. It is wrong: it looks like the embryo of the class.

Is the process always the same?

No. It is a general tendency; some steps are skipped, some don't even happen. However, there is never a reverse process. A bird never starts developing as a mammal.

Reminder:

Vertebrates are: Eukarya (domain), Animalia (kingdom), Chordata (phylum). Vertebrates include birds, fish, amphibians, reptiles and mammals.

Why do all embryos start developing in the same way?

It is due to evolution: the embryos of vertebrates seem to develop following the order in which species evolved. Our very ancient ancestor was rather fish-like than mammal-like. And we keep traces of this ancestor: in our genome. The growth of the embryo starts with the very ancient (fishy) genes, and "newer" (in an evolutionary meaning) genes activate later on during the growth.

Why do embryos not just skip the "useless" steps of their development?

The modifications of the species (not just as embryos, but seen in a long-lasting evolutionary process) turn old patterns into newer ones. Skipping the older model of development can be dangerous, since the latter showed itself as being well-built. Some bones could be crossed, nerves knotted, etc. Please refer to the next section, "Bad Design", for more details.

Bad Design

The design of a species is far from perfect: it is even the inverse. Imperfection is, however, the mark of and the proof for evolution: for this reason, bad design is normal. Bad design is a trait which is badly, not logically, even unnaturally built.

What does evolution have to do with bad design?

A necessary feature of a species may evolve, though it was functioning well. Organs are never independent; thus, if a necessary and well-working organ A is linked with organs B, C and D, and if organs B and C show more useful, more favourable to the species's survival, in another shape, the individuals having these favourable traits will survive better and reproduce more; the trait will be inherited by the offspring. Now, let's assume that, because of B and C's evolution, D becomes useless: it might become vestigial, or disappear. A, however, is still needed; but B and C's evolution demands to A to change. A will have to adapt (mainly its shape), but in a way that makes the end-result look bizarre, just unnatural, for nature develops in the most economical way; the trait is seen as a waste (of matter, of energy, etc.).

When does bad design occur?

Bad design is due to evolution, a long-lasting process (millions of years), over hundreds of generations. The modification from original to modern trait is often replayed during the development of the embryo (cf. Palimpsests in embryos.).

Why do badly designed traits not simply evolve into well-designed traits?

Each bad design is potentially dangerous, and it is in each case a waste, a nonsense. However, bad designs never repair. It is due to the muddled configuration of the problematic complex. The laryngeal nerve is a good example. In our fish-like embryos, this nerve connects the brain to the gills. This arch is not found in born humans (cf. palimpsests in embryos). The nerve is, however. In fish-like embryos, the laryngeal nerve passes behind the sixth branchial arch; the latter is not found in humans, since it has evolved. The laryngeal nerve had to adapt, and instead of simply connecting the brain to the larynx (into which the former part of the fish-like embryo has developed), it connects them but with a hook around the ligamentum arteriosum, which formerly was the sixth branchial arch. In fact, the nerve follows its ancient path, but handling with the new layout. Because of the hook, which is useless, and even maladaptive, we say the nerve (its true name is recurrent laryngeal nerve (from Latin, which comes back)) is a bad design.

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WEIT 2012 Chap3