5. The Evidence for the Theory is Irrefutable ==>
   5.1. Direct Evidence ==>
     5.1.5. Macroevolution ==> 21 Proofs Of Macroevolution*
*(One does not have to understand anything presented on this page.
The point is, there ARE people who DO understand this
AND it is FUNDAMENTAL to their discipline).

(1) Convergence of independent phylogenies.

Since there is one true historical phylogenetic tree, all separate lines

of evidence should converge on the same tree, what I call the standard

phylogenetic tree.


The phylogenetic tree determined by taxonomic analysis matches well the

phylogenetic tree constructed from protein, DNA, and ribosomal RNA

sequences. Because of the fact of DNA coding redundancy, parts of

certain DNA sequences can be chosen that have absolutely no correlation

with phenotype. These DNA sequences thus constitute independent data

from morphology


There are over 10^36 different possible ways to arrange the 29 major phyla (i.e. classes of

organisms) into a phylogenetic tree. In spite of the odds, the exact

relationships were independently determined from morphological

characters and from molecular studies.

Potential Falsification:

When it became possible to sequence biological molecules, the

realization of a markedly different phylogenetic tree based on the

independent molecular evidence would have been a fatal blow to the

theory of evolution, even though that is by far the most likely result.

Any alternate hypothesis to common descent must explain why a taxonomic

tree and a molecular tree corroborate each other, even though their is

no a priori correlation between the two (that is, besides heredity).

(2) A "nested" hierarchical organization of species.


Due to the hypothesis of common descent, the predicted pattern of

organisms at any given point in time can be described as "groups within

groups." This nested hierarchical organization of species is in

contrast to the continuum of "the great chain of being" and the

continuum predicted by Lamarcks theory of organic progression.


Few other natural processes would predict a hierarchical nested

classification. Real world examples that cannot be classified as such

are elementary particles (which are described by quantum chromodynamics

or QCD), the elements (whose organization is described by quantum

mechanics and illustrated by the periodic table), the planets in our

Solar System, books in a library, or specially designed objects like

buildings, furniture, cars, etc. That organisms merely can be related

to each other is not enough to support macroevolution; the nested

classification pattern that satisfies the macroevolutionary process is

very specific. It is interesting to note that human languages, which

have common ancestors and are derived by descent with modification,

generally can be classified in nested hierarchies.


Most existing species can be organized easily in a nested hierarchical

classification. This is evident in the use of the Linnaean

classification scheme. Based on shared derived characters, closely

related organisms can be placed in one group (such as a genus), several

genera can be grouped together into one family, several families can be

grouped together into an order, etc.


As a specific example, plants can be classified as vascular and

nonvascular (i.e. they have xylem and phloem). Nested within the

vascular group, there are two divisions, seed and non-seed plants.

Further nested within the seed plants are two more groups, the

angiosperms (which have enclosed, protected seeds) and the gymnosperms

(having non-enclosed seeds). Within the angiosperm group are the

monocotyledons and the dicotyledons.



Few species are ever found that combine characteristics of different

nested groupings. Proceeding with the previous example, some

nonvascular plants could have seeds or flowers, like vascular plants,

but they do not. Gymnosperms (e.g. conifers or pines) occasionally

could be found with flowers, but they never are. Non-seed plants, like

ferns, could be found with woody stems; however, only some angiosperms

have woody stems.


Conceivably, some birds could have mammary glands or hair; some mammals

could have feathers (they are an excellent means of insulation).

Certain fish or amphibians could have differentiated or cusped teeth,

but these are only characteristics of mammals. A mix and match of

characters like this would make it extremely difficult to organize

species into nested hierarchies.


If it were impossible, or very problematic, to place species in a nested

classification scheme (as it is for the various examples mentioned

above), macroevolution would be effectively disproven. Keep in mind

that the majority of species has been discovered since Darwins

hypothesis of common ancestry, and each new one found is a test of the

theory. Even so, they all have fit the correct pattern.


Any alternate hypothesis concerning lifes origins must also explain

this pattern, and it must also show how it could be falsified.

(4) Morphologies of predicted common ancestors.

Any fossilized animals found should conform to the standard phylogenetic

tree. What I refer to as the standard phylogenetic tree is the

consensus phylogeny of species based on taxonomic and molecular

evidence. Figure I, representing part of it, can be found here:


Every node shared between two branches represents a predicted common

ancestor; thus there are ~30 common ancestors predicted from the tree

shown in Figure I. Our standard tree shows that the bird grouping is

most closely related to the reptilian grouping, with a node linking the

two (A in Figure I); thus we predict the possibility of finding fossil

intermediates between birds and reptiles. The same reasoning applies to

mammals and reptiles (B in Figure I). However, we predict that we

should never find fossil intermediates between birds and mammals.

Additionally, each predicted common ancestor has a set of explicitly

specified morphological characteristics, based on all the most common

derived characters of its descendants. From the knowledge of avian and

reptilian morphology, it is possible to predict the characteristics that

a bird/reptile intermediate should have, if found. Therefore,

pterodactyl fossils are not considered possible candidates. However, we

do expect the possibility of finding reptile-like fossils with feathers,

bird-like fossils with teeth, or bird-like fossils with long reptilian



In this example, we have found a quite complete set of dinosaur-to-bird

transitional fossils represented by Sinosauropteryx, Protarchaeopteryx,

Caudipteryx, Archaeopteryx, and Confuciusornis, among many others, all

with the expected possible morphologies. We also have an exquisitely

complete series of fossils for the reptile/mammal intermediates, ranging

from the Pelycosauria, Therapsida, Cynodonta, up to primitive Mammalia.

There are many other examples such as these.

Potential falsifications:

Any finding of mammal/bird intermediates would be inconsistent. Many

other examples of prohibited intermediates can be thought of, based on

the standard tree.

Any hypothesis of design must also explain these data, and to be

considered scientifically it must make predictions like the theory of

common descent has. Also, there must be observations that would falsify

it, similar to the examples given above for the theory of common


(5) Chronological order of predicted common ancestors.

Fossilized intermediates should appear in the correct general

chronological order based on the standard tree. Any phylogenetic tree

predicts a relative chronological order of hypothetical common ancestors

and intermediates between these ancestors. For instance, in our current

example, a Figure of which can be found at


the reptile/mammal common ancestor (B) and intermediates should be older

than the reptile/bird common ancestor (A) and intermediates.


The reptile/bird intermediates mentioned above date from the Upper

Jurassic and Lower Cretaceous, whereas Pelycosauria and Therapsida are

older and date from the Carboniferous and the Permian.

Potential Falsification:

It would be inconsistent if the chronological order were reversed in

these two examples. Similarly, we never expect to find mammalian or

avian fossils in or before Devonian deposits, before reptiles had

diverged from the amphibian tetrapod line. This excludes Precambrian,

Cambrian, Ordovician, and Silurian deposits, encompassing 92% of the

earth's geological history and 65% of the biological history of

multicellular organisms. Even one incontrovertible find of a

pre-Devonian mammal or bird would shatter the theory of common descent.

One may object that this proof from the fossil record is merely

technically consistent with macroevolution, but is not true proof or

substantiation. However, what we require in science is precisely

technical consistency. Consistency is a major component of scientific

proof; according to Karl Popper it *is* proof, since according to his

falsificationist philosophy successful theories are the ones that have

not been falsified by evidence (i.e. they have remained consistent with

the evidence).

Likewise, one might say, "homology is entirely consistent with

creationism, but you won't say for a second that this *establishes* or

*demonstrates* creationism."

There is a very important difference here that is absolutely key, and it

nicely illustrates why most creationism or ID theories are rather

unscientific. Of course these results (i.e. homology and the fossil

record) would be entirely consistent with creationism - but could any

observation of homology or the lack thereof in biology falsify

creationism? Could any observation in the fossil record falsify


Thus, macroevolution wins the contest for scientific robustness, and ID

and creationism lose, precisely because macroevolution could be

falsified by the fossil record, and creationism cannot.

(6) Anatomical vestigial characters.

Some of the more renowned evidences for evolution are the explanations

it provides for vestigial characters, both anatomical and molecular.

Throughout macroevolutionary history, functions have been gained and

lost; thus we predict vestigial structures, which are structural

evidence of lost functions. Nonfunctional characters of organisms are

especially puzzling, for there is no apparent reason for their

existence. Thus evolutionary explanations for nonfunctional

attributes are strong proofs.


There are many examples of useless or nonfunctional characters of

organisms, and these can very often be explained in terms of

evolutionary histories. Some examples are the four fused tail

vertebrae of humans, the vestigial pelvises of pythons, the

rudimentary, nonfunctional legs found in some species of whales and

lizards, the eyes displayed by cave dwelling fishes in every stage of

degeneration, and the wings of flightless beetles retained underneath

fused wing covers. All of these examples can be explained in terms of

the functions and structures of the organism's predicted ancestors.

Potential Falsifications:

Shared derived characters (from cladistic analysis)

and molecular sequence data determine the

phylogeny and thus the characteristics of predicted common ancestors.

It follows that vestigial characters very possibly could lack an

evolutionary explanation.

For example, whales are classified as

mammals according to many criteria, such as having mammary glands, a

placenta, one bone in the lower jaw, etc. Snakes likewise are

classified as reptiles by several other derived features. However, it

is theoretically possible that snakes or whales could have been

classified as fish (Linnaeus originally made this error with the case of

whales). If this were the case, the vestigial legs of

whales or the vestigial pelvises of snakes would make no sense

evolutionarily, and would count as a falsification.

In fact, no organism can have a vestigial structure that was not

previously functional in one of its ancestors. Thus, for each

species, the standard phylogenetic tree makes a huge number of

predictions about vestigial characters that are allowed and those that

are impossible.

For instance, we should never find a vestigial placenta or vestigial

nipples in any amphibians, birds, or reptiles. No mammals should be

found with a vestigial breastbone (but they can have vestigial tails,

like humans do). We should never find any arthropods with vestigial

backbones. Note that this argument is not falsified by finding a

function for the presumed vestigial structure. If this happens, the

structure merely becomes an example of paralogy, which I will consider

in a later proof of macroevolution.

(7) Molecular vestigial characters.

Throughout macroevolutionary history, functions have been gained and

lost; thus we predict vestigial structures, which are structural

evidence of lost functions. Nonfunctional characters of organisms are

especially puzzling, for there is no apparent reason for their


Vestigial characters should also be found at the molecular level.

Humans do not have the capability to synthesize ascorbic acid (otherwise

known as Vitamin C), and the unfortunate consequence can be the

nutritional deficiency called scurvy. However, the predicted ancestors

of humans had this function (as do all animals except primates and

guinea pigs). Therefore, we predict that humans, primates, and guinea

pigs should carry evidence of this lost function as a vestigial



Recently, the L-gulano-gamma-lactone oxidase gene, the gene required for

Vitamin C synthesis, has been found in humans and guinea pigs. It

exists as a pseudogene, present but incapable of functioning (in a later

proof I will further consider pseudogenes).

There are several other examples of vestigial human genes, including

multiple odorant receptor genes, the RT6 protein gene, and the

galactosyl transferase gene. Our odorant receptor genes once coded for

proteins involved in now lost olfactory functions (our predicted

ancestors, like other mammals, had a more acute sense of smell than

us). The RT6 protein is expressed on the surface of T lymphocytes in

other mammals, but not on ours. The galactosyl transferase gene is

involved in making a certain carbohydrate found on the cell membranes of

other mammals.

It is also interesting to note that we share these three other vestigial

genes with other primates, and that the mutations that made these genes

nonfunctional are also shared with primates.

Potential Falsification:

It would be very puzzling if we had not found the L-gulano-gamma-lactone

oxidase pseudogene or the other vestigial genes mentioned. In addition,

we can predict that we will never find vestigial chloroplast genes in

any metazoans (i.e. animals).

(1) The fundamental unity of life.

Modern living organisms, with all their incredible differences, are the

progeny of one single species in the distant past. In spite of their

extensive variation of form and function, there are several fundamental

criteria that characterize life. Some of the macroscopic properties

that characterize all of life are (1) replication, (2) information flow

in continuity of kind, (3) catalysis, and (4) energy utilization

(metabolism). At a very minimum, these functions are required to

generate a historical process that can be described by a phylogenetic


The genealogical relatedness of all life predicts that organisms should

be very similar in the particular mechanisms and structures that execute

these basic life processes. If every living species descended from one

original species, all living organisms should have inherited the

structures and mechanisms that perform these very basic necessary



Organic chemists have synthesized hundreds of different polymers, yet

the only ones used by life, irrespective of species, are

polynucleotides, polypeptides, and polysaccharides. All of life uses

the same molecule, DNA, for storing species specific information. All

organisms base replication on the duplication of this molecule. The DNA

used by living organisms employs only four bases (adenine, thymidine,

cytosine, and guanine) out of the dozens known ( target="_blank">>80 occur naturally and

many have been artificially synthesized).

All organisms perform enzymatic catalysis with protein molecules (and in

rare cases with RNA molecules). There are about 250 naturally occurring

amino acids; the protein molecules used by all living organisms are

constructed with the same twenty amino acids.

There must be a mechanism for transmitting information from the genetic

material to the catalytic material; all organisms, with extremely rare

exceptions, use the same genetic code for this.

Regardless of the species, DNA, RNA and proteins all have the same

chirality, even though there are at least two equivalent choices of

chirality for each of these molecules.

All organisms use extremely similar, if not the same, metabolic pathways

and metabolic enzymes in processing energy-containing molecules. For

example, the fundamental metabolic systems in living organisms are

glycolysis, the citric acid cycle, and oxidative phosphorylation. In

all eukaryotes and in the majority of prokaryotes, glycolysis is

performed in the same ten steps, in the same order, using the same ten

enzymes. In addition, the most basic unit of energy storage, the

adenosine triphosphate molecule (ATP), is the same in all species.

Potential Falsifications:

It was not too long ago that the identity of the genetic material of

life was unknown. It is quite conceivable that there could be a

different genetic material for each species or that there could be

species specific genetic codes (there are millions upon millions of

functionally equivalent genetic codes using the same codons and amino


Another possibility is that each species could use a different polymer

for catalysis. The polymers that are used could still be chemically

identical yet have different chiralities in different species.

There are thousands of thermodynamically equivalent glycolysis pathways

(even using the same ten reaction steps but in different orders), so it

is possible that many species could have their own specific glycolysis

pathways, tailored to their own unique needs.

Finally, many molecules besides ATP could serve equally well as the

common currency for energy in various species (CTP, TTP, UTP, ITP, or

any ATP-like molecule with one of the 250 known amino acids or one of

the 80 other bases replacing the adenosine moiety immediately come to


Any of these would be strong disproofs of common ancestry, but they have

not been found. For instance, suppose we were to check the genetic code

of an organism that has not been studied rigorously (say, an iguana, or

a newly found species from the Brazilian rainforest). It is quite

possible that the genetic code for this species could be radically

different from the "standard" genetic code. Actually, this is what is

probable from statistical analysis. If this were found to be true, it

would be a strong falsification of macroevolution.

Additionally, since these macroevolutionary predictions have been

confirmed, any competing theory must also explain these data.

Proof of Macroevolution: (8) Evidence from Ontogeny

Embryology and developmental biology have provided some fascinating

insights into evolutionary pathways. Since the taxonomic classification

of species is generally based on derived characters of adult organisms,

embryology and developmental studies provide an independent body of

evidence. The early history of embryology was greatly influenced by the

ideas of Ernst Haeckel; however, his ideas have been superseded by those

of Karl Ernst van Baer, his predecessor. Van Baer suggested that the

embryonic stages of an individual should resemble the embryonic stages

of its ancestors (rather than resembling its adult ancestors, a la


The final adult structure of an organism is the product of numerous

cumulative developmental processes; for species to evolve, there

necessarily must have been change in these developmental processes. The

macroevolutionary conclusion is that the development of an organism is a

modification of its ancestors ontogenies.

The modern developmental maxim is the inverse of Haeckels biogenetic

law. Phylogeny recapitulates Ontogeny, not the opposite. What this

means is that once given knowledge about an organism's ontogeny, we can

confidently predict certain aspects of the historical pathway that was

involved in this organism's evolution. Thus, embryology can provide

confirmations and predictions about evolution.


From embryological studies it is known that two bones of a developing

reptile eventually form the quadrate and the articular bones in the

hinge of the adult reptilian jaw. However, in the marsupial mammalian

embryo, the same two structures develop, not into parts of the jaw, but

into the anvil and hammer of the mammalian ear. This suggests that in

evolution, the mammalian ear was derived from the reptilian jaw.

Accordingly, there is a very complete series of fossil intermediates in

which these structures are clearly modified from the reptilian jaw to

the mammalian ear. There are numerous other examples where an

organism's evolutionary history is represented temporarily in its

development, such as mammalian gill pouches and avian teeth.

Potential Falsification:

We may expect to find gill pouches in mammalian embryos, based on our

standard phylogenetic tree, but we never expect to find nipples or hair

in fish, amphibian, or reptilian embryos. Likewise, we might expect to

find teeth in the mouths of avian embryos, but we never expect to find

beaks in eutherian mammal embryos.

(9) Present biogeography.

Because species divergence happens not only in the time dimension, but

also in spatial dimensions, common ancestors originate in a particular

geographical location. Thus, the spatial and geographical distribution

of species should be consistent with their predicted genealogical

relationships. The standard phylogenetic tree predicts that new species

must originate close to the older species from which they are derived.

Closely related contemporary species should be close geographically,

regardless of their habitat or specific adaptations. If they are not,

there had better be a good explanation, such as extreme mobility (cases

like sea animals, birds, human mediated distribution, etc.), continental

drift, or extensive time since their divergence. A reasonable

nonevolutionary prediction is that species should occur wherever their

habitat is. However, macroevolution predicts just the opposite - there

should be many locations where a given species would thrive but it is

not found there, due to geographical barriers.


With few exceptions, marsupials only inhabit Australia. The exceptions

(some South American species and the opossum) are explained by

continental drift (South America, Australia, and Antarctica were once

the continent of Gondwanaland).

Conversely, placental mammals are virtually absent on Australia, despite

the fact that many would flourish there. Most of the few placentals

found on Australia were introduced by humans, and they have spread


Similarly, the southern reaches of South America and Africa and all of

Australia share lungfishes, ostrich-like birds (ratite birds), and

leptodactylid frogs - all of which occur nowhere else.

Alligators, some related species of giant salamander, and magnolias only

occur in Eastern North America and East Asia (these two locations were

once spatially close in the Laurasian continent).

In addition, American, Saharan and Australian deserts have very similar

habitats, and plants from one grow well in the other. However,

indigenous Cacti only inhabit the Americas, while Saharan and Australian

vegetation is very distantly related (mostly Euphorbiaceae). The only

Cacti found in the Australian outback were introduced by humans, and

they grow quite well in their new geographical location.

The west and east coast of South America is very similar in habitat, but

the marine fauna is very different. In addition, members of the closely

related pineapple family inhabit many diverse habitats (such as

rainforest, alpine, and desert areas), but only in the American tropics,

not African or Asian tropics.

Potential Falsification:

From a limited knowledge of species distributions, we predict that we

should never find elephants on Hawaii, or any other undiscovered

islands, even though they would survive well there. Similarly, we

predict that we should not find amphibians on remote islands, or

indigenous Cacti on Australia. Closely related species could be

distributed evenly worldwide, according to whichever habitat best suits

them. If this were the general biogeographical pattern, it would be a

strong blow to macroevolution.

Proof of Macroevolution: (10) Past biogeography.

Past biogeography, as recorded by the fossils that are found, must also

conform to the standard phylogenetic tree -


Thus we predict that fossils of the hypothetical common ancestors of

South American marsupials and Australian marsupials should be found

before these two landmasses separated.


Consequently, we find the earliest marsupial fossils (e.g., Alphadon)

from the Late Cretaceous, when South America, Antarctica, and Australia

were still connected. Additionally, the earliest ancestors of

marsupials are actually found on North America, and the paleontological

prediction from this is that extinct marsupials fossil organisms should

be found on South America and Antarctica, since marsupials must have

traversed these continents to reach their present day location in

Australia. Interestingly, we have found marsupial fossils on both

South America and on Antarctica. This is an astounding

macroevolutionary confirmation, given that no marsupials live on

Antarctica now.

Potential Falsification:

We confidently predict that fossils of recently evolved animals like

apes and elephants should never be found on South America, Antarctica,

or Australia.

As a second example, very complete fossil records should be smoothly

connected geographically. Intermediates should be found close to their

fossil ancestors.


The Equidae (i.e. horse) fossil record is very complete (though

extremely complex) and makes very good geographical sense, without any

large spatial jumps between intermediates. For instance, at least ten

intermediate fossil horse genera span the past 58 million years. Each

fossil genus spans approximately 5 million years, and each of these

genera includes several intermediate paleospecies (usually 5 or 6 in

each genus) that link the preceding and following fossil intermediates.

They range from the earliest genus, Hyracotherium, which somewhat

resembled a dog, through Orohippus, Epihippus, Mesohippus, Miohippus,

Parahippus, Merychippus, Dinohippus, Equus, to Modern Equus. Every

single one of the fossil ancestors of the modern horse are found on the

North American continent.

Potential Falsification:

It would be macroevolutionarily devastating if we found in South America

an irrefutable Epihippus or Merychippus (or any of the intermediates

in-between) from the Paleocene, Eocene, Oligocene, the Miocene, or

anytime before the isthmus of Panama arose to connect North and South

America (about 12 million years ago). Moreover, we should never find

fossil horse ancestors on Australia or Antarctica from any geological

era. Proof of Macroevolution: (12) Molecular paralogy.

The concept of paralogy applies equally to both the macroscopic

structures of organisms and structures on the molecular level.

Paralogy, as I use the term here, is similarity of structure despite

difference in function.


On the molecular level, the existence of paralogy is quite impressive.

Many proteins of very different function have strikingly similar amino

acid sequences and three-dimensional structures. A frequently cited

example is lysozyme and alpha-lactalbumin. Lysozyme is found in almost

all animals. It is a secreted protein used to degrade bacterial cell

walls as a means of defense. Alpha-lactalbumin is very similar

structurally to lysozyme, even though its function is very different (it

is involved in lactose synthesis). It can often be shown from molecular

phylogenies, as it has been here, that the protein with the more basic

function (e.g. lysozyme) is also the older protein.

On a grander scale, a stunning confirmation of these evolutionary

predictions has come from an analysis of Saccharomyces cerevisiae

(bakers yeast) and Caenorhabditis elegans (a worm). The genomes of

both these organisms were sequenced very recently. The genes used by

the yeast, a unicellular organism, are mostly genes dealing directly

with core biochemical functions that all organisms must perform. From

an evolutionary perspective we would expect these genes to be ancient.

Thus it was expected and shown that the worm contains a great majority

of these genes. In contrast, the extra genes used by the worm, which

deal with multicellularity, should be more recently evolved.

Phylogenetic analysis has shown that this is exactly the case. The vast

majority of extra genes in the worm appear to be directly derived from

genes providing core cellular functions, in accordance with evolutionary



Proteins performing more recently evolved functions should have

homologues with proteins performing core functions. It is

evolutionarily problematic if they do not (however, there a few rather

rare mechanisms known for generating novel proteins). Furthermore, it

would be inconsistent with evolutionary theory if we had found that

genes involved in multi-cellular functions were more deeply rooted in

their phylogenies than genes involved with core functions (i.e., if

these genes were more ancient than the core function genes).

Proof of Macroevolution: (13) Anatomical convergence.

A corollary of the principle of evolutionary opportunism is

convergence. Convergence is the case where the same or similar

functions are performed by different structures. Two distinct species

have different histories and different structures; if both species

evolve the same new function, they may recruit different structures to

perform this new function. Since all convergence is paralogy,

convergence also must conform to the principle of structural

continuity. Convergence must be explained in terms of the structures of

predicted ancestors.


There are many anatomical examples of functional convergence. One case

is the vertebrate eye and the cephalopod eye. Another, mentioned

earlier, is the case of American and Saharan desert plants, which use

different structures for the same functions needed to live in dry, arid

regions. Certain mammals (whales, manatees, dolphins), birds

(penguins), and fish all have the ability to live and swim in aquatic

environments, and they obviously use different structures overall for

these aquatic functions. Although now modified, all of the structures

that perform these functions are also present in their predicted


Potential Falsification:

We would not expect any adult dolphins or penguins to have gills (a

possible convergence with fish), since their immediate ancestors lacked


Paralogy and convergence are specific predictions of macroevolution and

the principle of evolutionary opportunism. It is possible that a world

could exist where there were no cases of biological paralogy or

convergence. As an example given in an earlier post, living organisms

could be constructed in a modular manner, like most anthropogenic

creations, where one specific structure performs one specific function. Proof of Macroevolution: (14) Molecular convergence.

Like paralogy, convergence should be represented on both macroscopic and

molecular levels.


A familiar molecular example is the case of the three proteases

subtilisin, carboxy peptidase A, and trypsin. These three proteins are

all serine proteases (i.e., they degrade other proteins in digestion).

They have the same function, the same catalytic residues in their active

sites, and they have the same catalytic mechanism. Yet they have no

sequence or structural homology.

Another molecular example is that of DNA polymerases. DNA polymerases

are the proteins that catalyze the duplication of a strand of DNA; i.e.

they catalyze multiple additions of nucleotides to a DNA strand. All

the structures determined for DNA polymerases have clear structural

similarity except for one, rat polymerase beta. Except for rat

polymerase beta, all the DNA polymerases are most likely related by

divergent evolution. Rat polymerase beta has structural homology with

nucleotidyl transferases, which catalyze the addition of one nucleotide

to a DNA strand. Rat polymerase beta has obviously evolved from

nucleotidyl transferases by mutating to catalyze several nucleotide

additions instead of just one (which nicely illustrates why convergence

is also paralogy).

Potential Falsification:

As mentioned previously, paralogy and convergence are specific

predictions of macroevolution and the principle of evolutionary

opportunism. It is possible that a world could exist where there were

no cases of biological paralogy or convergence. For example, living

organisms could be constructed in a modular manner, like most

anthropogenic creations, where one specific structure performs one

specific function.

Proof of Macroevolution: (14) Molecular convergence.

Like paralogy, convergence should be represented on both macroscopic and

molecular levels.


A familiar molecular example is the case of the three proteases

subtilisin, carboxy peptidase A, and trypsin. These three proteins are

all serine proteases (i.e., they degrade other proteins in digestion).

They have the same function, the same catalytic residues in their active

sites, and they have the same catalytic mechanism. Yet they have no

sequence or structural homology.

Another molecular example is that of DNA polymerases. DNA polymerases

are the proteins that catalyze the duplication of a strand of DNA; i.e.

they catalyze multiple additions of nucleotides to a DNA strand. All

the structures determined for DNA polymerases have clear structural

similarity except for one, rat polymerase beta. Except for rat

polymerase beta, all the DNA polymerases are most likely related by

divergent evolution. Rat polymerase beta has structural homology with

nucleotidyl transferases, which catalyze the addition of one nucleotide

to a DNA strand. Rat polymerase beta has obviously evolved from

nucleotidyl transferases by mutating to catalyze several nucleotide

additions instead of just one (which nicely illustrates why convergence

is also paralogy).

Potential Falsification:

As mentioned previously, paralogy and convergence are specific

predictions of macroevolution and the principle of evolutionary

opportunism. It is possible that a world could exist where there were

no cases of biological paralogy or convergence. For example, living

organisms could be constructed in a modular manner, like most

anthropogenic creations, where one specific structure performs one

specific function.

Proof of Macroevolution: (15) Anatomical suboptimal function.

Another consequence of evolutionary opportunism (see post 11 and

follow-ups) is the existence of apparent suboptimal function. As stated

before, in evolving a new function, organisms must make do with what

they already have. Thus functions are likely to be performed by

structures that would be arranged differently (e.g., more efficiently)

if the final function were known from the outset. Suboptimal function

should be explainable in terms of evolutionary histories.


The mammalian gastrointestinal tract crosses the respiratory system.

This is why we are susceptible to choking. Functionally, this is

suboptimal. However, there is a good historical evolutionary reason for

this arrangement. The lungfishes, from which mammals evolved, swallow

air to breathe. Only later did mammals recruit the olfactory nares of

fish for the function of breathing on land. It so happens that the

nares (originally used for smelling) are on the opposite side of the

esophagus from the lungs.

Another anatomical example of suboptimal function is the mammalian

retina, with its blind spot. Cephalopods have eyes based on the same

mechanistic principles as mammalian eyes. However, cephalopodian eyes

have very different underlying retinal structures, and they have no

blind spots.


Structures with suboptimal function should have a historical

evolutionary explanation, based on the opportunistic recruitment of

ancestral structures. If they presently do not, it is not an especially

strong falsification since negative evidence is the weakest class of

scientific evidence. However, if this were the general pattern (i.e.,

there were no plausible evolutionary explanations for the poor

functional designs in the majority of organisms), it would be quite

suspicious. Luckily this is not the case.

More strongly, a positive falsification would be the discovery of any

mammal without crossed gastrointestinal and respiratory tracts, or

without blindspots in its eyes, etc. This is because poor design cannot

be fixed by evolutionary processes, even if correcting the problem

would be beneficial for the organism. The only fixing that is allowed

evolutionarily is relatively minor modification of what already exists.

Proof of Macroevolution: (16) Molecular suboptimal function.

The principle of imperfect design should apply to biomolecular

organization as well (see the link below for my last post on the



We find that only 2% of the DNA in the human genome is used for making

proteins. 25% is comprised of transposons, which serve no function for

the individual (except to cause occasional genetic illnesses and

increase the rate of cancer formation). 20% of the human genome is

pseudogenes. They also serve no function for the individual. A

remarkable example is the glyceraldehyde-3-phosphate dehydrogenase

(GDPH) gene. In humans, there is one functional GDPH gene, but there

are at least twenty GDPH pseudogenes. In mice, there are approximately

200 GDPH pseudogenes, none of which are necessary.

The majority of eukaryotic genes coding for functional proteins are

interrupted by noncoding sequences called introns. Introns must be cut

out before the information contained in the gene can be used to make

protein. Introns make up 80% of the average human gene. Similar to

transposons, most introns serve no purpose (in rare cases they are

involved in gene regulation or code for a functional RNA).

The rest of the DNA in a eukaryotic genome is mostly short repetitive

sequences that likewise serve no function, and they have even been

termed junk DNA. It appears that there is no efficient mechanism for

ridding a metazoan (animal) genome of extraneous DNA; once extra DNA is

introduced into the genome of an animal, it is there to stay.

Even protists, unicellular organisms, are subject to such evolutionary

jerry-rigging. Two ciliates, Paramecium aurelia and Paramecium

caudatum, are virtually indistinguishable from morphological and

phenotypic analysis, and they contain the same number of functional

proteins. However, the first has less than 200,000 kb of DNA in its

genome, whereas the genome of the second has nearly 9,000,000 kb of DNA,

which is evidently 45 times the amount it needs.

There is a lot of wasted energy expended in dealing with this useless

DNA; however, all these molecular examples also have convincing

explanations based on evolutionary histories.

Potential Falsification:

Because evolution has no foresight, and cannot plan for future

functions, it would be extremely suspicious if biological molecular

systems were efficiently designed. This does not rule out complexity,

merely efficiency of mechanism.

Proof of Macroevolution: (18) Functional molecular evidence - DNA

coding redundancy.

Like protein sequence similarity, the DNA sequence similarity of two

ubiquitous genes also implies common ancestry. Of course, comprehensive

DNA sequence comparisons of conserved proteins such as cytochrome c also

indirectly take into account amino acid sequences, since the DNA

sequence specifies the protein sequence.

However, with DNA sequences there is an extra level of redundancy. The

genetic code itself is informationally redundant; on average there are 3

different codons (a codon is a triplet of DNA bases) that can specify

the exact same amino acid. Thus, for cytochrome c there are 3^104, or

over 10^49, different DNA sequences (and, hence, 10^49 different

possible genes) that can specify the very exact same protein sequence.


As mentioned above, the cytochrome c proteins in chimps and humans are

exactly the same. The clincher is that the two DNA sequences that code

for cytochrome c in humans and chimps differ by only one codon, even

though there are 10^49 different sequences that could code for these two


Thus, there are really just two choices. Either, (1) from probability

considerations, we are highly confident that humans and chimps are

closely genealogically related, or (2) a designer chose the two DNA

sequences out of the over 10^49 informationally equivalent possibilities

that make it look exactly like we are genealogically related.

The combined effects of DNA coding redundancy and protein sequence

redundancy make DNA sequence comparisons doubly redundant; DNA sequences

of ubiquitous proteins are completely uncorrelated with phenotype, but

they are strongly correlated with heredity. This is why DNA sequence

phylogenies are considered so robust.


The most probable result is that the DNA sequences coding for these

proteins should be radically different. This would be a resounding

falsification of macroevolution, and it would be very strong proof that

chimpanzees and humans are not closely genealogically related. (19) Nonfunctional molecular evidence -


Transposons are very similar to viruses. However, they lack genes for

viral coat proteins, cannot cross cellular boundaries, and thus they

replicate only in the genome of their host. They can be thought of as

intragenomic parasites.

Except in the rarest of circumstances, the only mode of transmission

from one organism to another is directly by DNA duplication and

inheritance (e.g. your transposons are given to your children).

Replication for a transposon means copying itself and inserting the

copied DNA randomly somewhere else in the host's genome. Transposon

replication (also called transposition) has been directly observed in

many organisms, including yeast, corn, wallabies, humans, bacteria, and

flies, and presently the mechanisms are well understood. In fact,

specific cases of retrotransposition are known to cause

neurofibromatosis and hemophilia in humans.

Finding the same transposon in the same chromosomal location in two

different species is direct evidence of common ancestry, since they

insert randomly and cannot be transmitted expect by inheritance. In

addition, once a common ancestor has been postulated that contains this

transposition, all the descendants of this common ancestor should also

contain the same transposition.


A common class of transposon is the SINE retroelement. One important

SINE transposon is the 300 bp Alu element. All mammals contain many Alu

elements, including humans where they constitute 5% of the human genome.

Very recent human Alu transpositions have been used to elucidate

historic and prehistoric human migrations, since some individuals have

newer Alu insertions that other individuals lack. Most importantly, in

the human alpha-globin cluster there are seven Alu elements, and each

one is shared with chimpanzees in the exact same seven locations.

More specifically, three different specific SINE transpositions have

been found in the same chromosomal locations of cetaceans (whales),

hippos, and ruminants, all of which are closely related according to the

standard phylogenetic tree. However, all other mammals, including

camels and pigs, lack these three specific transpositions.

These examples are direct evidence of common ancestry between the

organisms that share these specific retrotransposons.

(20) Nonfunctional molecular evidence -


Another nonfunctional molecular example that provides evidence of common

ancestry is pseudogenes. Pseudogenes are very closely related to their

functional counterparts (in primary sequence and often in chromosomal

location), except that they have either faulty regulatory sequences or

they have internal stops that keep the protein from being made. They

are functionless and do not affect an organism's phenotype when deleted.

Pseudogenes, if they are not vestigial (like the examples in proof 7),

are created by gene duplication and subsequent mutation (there are many

observed processes that duplicate genes, including transposition events,

chromosomal duplication, and unequal crossing over of chromosomes).

Like transpositions, gene duplication is a rare and random event, and of

course any duplicated DNA is inherited. Thus, finding the same

pseudogene in the same chromosomal location in two species is strong

evidence of common ancestry.


There are very many examples of shared pseudogenes between primates and

humans. One is the psi-eta-globin gene, a hemoglobin pseudogene. It is

shared among the primates only, in the exact chromosomal location, with

the same mutations that render it non-functional. Another example is

the steroid 21-hydroxylase gene. Chimps and humans both share the same

8 bp deletion in this gene that renders it nonfunctional.