Science, Just Science

24 April 2007

Evolutionary Predictions

Filed under: Creationism & Intelligent Design,Science — Kyuuketsuki @ 2:46 pm

*** Originally posted by Tim Hague on SJS ***

Introduction

A point was made by a contributor in the SJS forums that we don’t mention anywhere on our site predictions made by the Theory of Evolution, yet we disparage ID for not making any predictions at all. This is a very good point – and a frequent and inaccurate claim by creationists is that “evolution doesn’t make predictions either”. This claim couldn’t be further from the truth.

This article presents just a few of the predictions that have been made using the Theory of Evolution. Included are some predictions by Darwin himself, some predictions that can be made using the theories of common descent and natural selection, and even some predictions that can be made using the theory of random mutation!

This article starts – appropriately enough – with some of Darwin’s predictions, then looks at one of the most powerful predictive theories within Evolution – common descent. Then there is a look at natural selection and random mutation. Finally we have a bit more from Darwin and a combination of both natural selection and common descent…

1. Darwin’s Predictions

When Darwin first published his thoughts on natural selection, he made very specific predictions about the time courses involved. Specifically, his theory required millions or billions of years, not thousands of years, to work. Darwins predictions about the time scales involved could have been disproven time and time again in the intervening years, however all the evidence collected both by biology and the other sciences – the fossil and geological evidence, radioactive dating, tectonic geological evidence, DNA evidence – all confirms Darwin’s prediction.

Darwin predicted that inheritance is particulate rather than just a blend of the parents characteristics. While Darwin’s theory of common ancestry was widely accepted by the late 1800’s, his theory of evolution by natural selection was actually considered to be disproven as of the end of the 1800’s and the beginning of the 20th century. Before the rediscovery of Mendel’s work, inheritance was thought to be blending rather than particulate. Mendel showed that inheritance is indeed particulate and so confirmed Darwin’s prediction.

Darwin acknowledged that the fossil record was incomplete – but as new discoveries were made he predicted that new transitional fossils would be found. New transitional fossils are still being discovered all the time. An excellent example of this are five new transitional fossils that have been discovered between land mammals and cetaceans (whales). These are particularly ironic, because creationists predicted that they would never be found!

2. Common Descent Predictions

Descent from a common ancestor entails a process of branching and divergence of species, in common with any genealogical process. Genealogies can be graphically illustrated by tree-like diagrams, and this is why you will hear biologists refer to the genealogy of species as the “tree of life”.

The most import common descent prediction of all:

The macroevolutionary prediction of a unique, historical universal phylogenetic tree is the most important, powerful, and basic conclusion from the hypothesis of universal common descent.

2.1 The fundamental unity of life

According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are:

  1. Replication
  2. Heritability (characteristics of descendents are correlated with those of ancestors)
  3. Catalysis
  4. Energy utilization (metabolism)

At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.

Thus, a basic prediction of the genealogical relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.

Confirmation:
The structures that all known organisms use to perform these four basic processes are all quite similar, in spite of the odds. All known living things use polymers to perform these four basic functions.

Potential Falsification:
Thousands of new species are discovered yearly, and new DNA and protein sequences are determined daily from previously unexamined species (over 20,000 new sequences are deposited at GenBank? every day). Each and every one is a test of the theory of common descent.

Based solely on the theory of common descent and the genetics of known organisms, we strongly predict that we will never find any modern species from known phyla on this Earth with a foreign, non-nucleic acid genetic material. We also make the strong prediction that all newly discovered species that belong to the known phyla will use the “standard genetic code” or a close derivative thereof.

When it became possible to sequence biological molecules, the realization of a markedly different tree based on the independent molecular evidence would have been a fatal blow to the theory of evolution. More precisely, the common descent hypothesis would have been falsified if the universal phylogenetic trees determined from the independent molecular and morphological evidence did not match with statistical significance.

2.2 Intermediate and transitional forms: the possible morphologies of predicted common ancestors

Our standard tree shows that the bird grouping is most closely related to the reptilian grouping, thus we predict the possibility of finding fossil intermediates between birds and reptiles. The same reasoning applies to mammals and reptiles. However, we predict that we should never find fossil intermediates between birds and mammals.

Confirmation:
bird-reptiles
We have found a complete set of dinosaur-to-bird transitional fossils with no morphological “gaps” represented by Eoraptor, Herrerasaurus, Ceratosaurus, Allosaurus, Compsognathus, Sinosauropteryx, Protarchaeopteryx, Caudipteryx, Velociraptor, Sinovenator, Beipiaosaurus, Sinornithosaurus, Microraptor, Archaeopteryx, Rahonavis, Confuciusornis, Sinornis, Patagopteryx, Hesperornis, Apsaravis, Ichthyornis, and Columba, among many others. All have the expected possible morphologies, including organisms such as Protarchaeopteryx, Caudipteryx, and the famous “BPM 1 3-13” which are flightless bipedal dinosaurs with modern-style feathers.

reptile-mammals
We also have an exquisitely complete series of fossils for the reptile-mammal intermediates, ranging from the pelycosauria, therapsida, cynodonta, up to primitive mammalia.

Potential Falsification:
Any finding of a striking half-mammal, half-bird intermediate would be highly inconsistent with common descent. Many other examples of prohibited intermediates can be thought of, based on the standard tree.

2.3 Anatomical vestiges

Some of the most renowned evidence for evolution are the various nonfunctional or rudimentary vestigial characters, both anatomical and molecular, that are found throughout biology. A vestige is defined, independently of evolutionary theory, as a reduced and rudimentary structure compared to the same complex structure in other organisms. Vestigial characters, if functional, perform relatively simple, minor, or inessential functions using structures that were clearly designed for other complex purposes. Though many vestigial organs have no function, complete non-functionality is not a requirement for vestigiality.

Vestigial structures have perplexed naturalists throughout history and were noted long before Darwin first proposed universal common descent. From common descent and the constraint of gradualism, we predict that many organisms should retain vestigial structures as structural remnants of lost functions. Note that the exact evolutionary mechanism which created a vestigial structure is irrelevant as long as the mechanism is a gradual one.

2.4 Molecular vestigial characters

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 most other animals except primates and guinea pigs). Therefore, we predict that humans, other primates, and guinea pigs should carry evidence of this lost function as a molecular vestigial character (nota bene: this very prediction was explicitly made by Nishikimi and others and was the impetus for the research detailed below)

Confirmation:
Recently, the L-gulano-γ-lactone oxidase gene, the gene required for Vitamin C synthesis, was found in humans and guinea pigs. It exists as a pseudogene, present but incapable of functioning. In fact the vitamin C pseudogene has now also been found in other primates, exactly as predicted by evolutionary theory. We now have the DNA sequences for this broken gene in chimpanzees, orangutans, and macaques. And, as predicted, the malfunctioning human and chimpanzee pseudogenes are the most similar, followed by the human and orangutan genes, followed by the human and macaque genes, precisely as predicted by evolutionary theory. Furthermore, all of these genes have accumulated mutations at the exact rate predicted (the background rate of mutation for neutral DNA regions like pseudogenes)

2.5 Present and past 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.

2.6 Anatomical parahomology

One major consequence of the constraint of gradualism is the predicted existence of parahomology. Parahomology, as the term is used here, is similarity of structure despite difference in function. Prediction: when one species branches into two species, one or both of the species may acquire new functions.

2.7 Molecular parahomology

Prediction: the concept of parahomology applies equally to both the macroscopic structures of organisms and structures on the molecular level.

Confirmation:
On the molecular level, the existence of parahomology is quite impressive. Many proteins of very different function have strikingly similar amino acid sequences and three-dimensional structures.

2.8 Anatomical analogy

A corollary of the principle of evolutionary opportunism is analogy. Analogy is the case where different structures perform the same or similar functions in different species. 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. Analogy also must conform to the principle of structural continuity; analogy must be explained in terms of the structures of predicted ancestors.

2.9 Molecular analogy

Prediction: like parahomology, analogy should be represented on both macroscopic and molecular levels.

2.10 Anatomical suboptimality

Prediction: Evolutionary opportunism also results in suboptimal functions and structures.

2.11 Molecular suboptimality

Prediction: The principle of imperfect design should apply to biomolecular organization as well.

2.12 Protein functional redundancy

Ubiquitous genes: There are certain genes that all living organisms have because they perform very basic life functions; these genes are called ubiquitous genes. Similar ubiquitous genes indicate genealogical relationship: It follows that organisms which have similar sequences for ubiquitous proteins are genealogically related. Roughly, the more similar the sequences, the closer the genealogical relationship.

2.13 DNA coding redundancy

Like protein sequence similarity, the DNA sequence similarity of two ubiquitous genes also implies common ancestry.

Here we can be quite specific in our prediction. Any sequence differences between two functional cytochrome c genes are necessarily functionally neutral or nearly so. As mentioned above, the cytochrome c proteins in chimps and humans are exactly identical. The clincher is that the two DNA sequences that code for cytochrome c in humans and chimps differ by only four nucleotides (a 1.2% difference), even though there are 1049 different sequences that could code for this protein.

2.14 Molecular evidence – Transposons

In many ways, 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 metazoan organism to another is directly by DNA duplication and inheritance (e.g. your transposons are given to your children)

Prediction: Finding the same transposon in the same chromosomal location in two different organisms is strong direct evidence of common ancestry, since they insert fairly randomly and generally cannot be transmitted except by inheritance.

Prediction: In addition, once a common ancestor has been postulated that contains a certain transposition, all the descendants of this common ancestor should also contain the same transposition.

2.15 Molecular evidence – Redundant pseudogenes

Other molecular examples that provide evidence of common ancestry are curious DNA sequences known as pseudogenes. Pseudogenes are very closely related to functional, protein-coding genes. The similarity involves both the primary DNA sequence and often the specific chromosomal location of the genes. The functional counterparts of pseudogenes are normal genes that are transcribed into mRNA, which is in turn actively translated into functional protein. In contrast, pseudogenes have faulty regulatory sequences that prevent the gene from being transcribed into mRNA, or they have internal stop codons that keep the functional protein from being made. In this sense, pseudogenes are molecular examples of vestigial structures.

Like transpositions, the creation of new redundant pseudogenes by gene duplication is a rare and random event and, of course, any duplicated DNA is inherited. Prediction: Thus, finding the same pseudogene in the same chromosomal location in two species is strong evidence of common ancestry.

2.16 Molecular evidence – Endogenous retroviruses

Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent. Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous retroviral sequences. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a DNA copy of their own viral genome and insert it into their host’s genome. If this happens to a germ line cell (i.e. the sperm or egg cells) the retroviral DNA will be inherited by descendants of the host. Prediction: Again, this process is rare and fairly random, so finding retrogenes in identical chromosomal positions of two different species indicates common ancestry.

2.17 Genetic change

The genetic information specifies everything about an organism and its potential. Prediction: Genotype specifies possible phenotypes, therefore, phenotypic change follows genetic change. This obviously should be one of the areas where evolutionary change is seen, and genetic change is truly the most important for understanding evolutionary processes.

Confirmation:
Extremely extensive genetic change has been observed, both in the lab and in the wild. We have seen genomes irreversibly and heritably altered by numerous phenomena, including gene flow, random genetic drift, natural selection, and mutation. Observed mutations have occurred by mobile introns, gene duplications, recombination, transpositions, retroviral insertions (horizontal gene transfer), base substitutions, base deletions, base insertions, and chromosomal rearrangements. Chromosomal rearrangements include genome duplication (e.g. polyploidy), unequal crossing over, inversions, translocations, fissions, fusions, chromosome duplications and chromosome deletions.

2.18 Morphological change

Cladistic classification, and thus, phylogenetic reconstruction, is largely based on the various distinguishing morphological characteristics of species. Macroevolution requires that organisms’ morphologies have changed throughout evolutionary history. Preduction: Thus, we should observe morphological change and variation in modern populations.

Confirmation:
There have been numerous observations of morphological change in populations of organisms. Examples are the change in color of some organ, such as the yellow body or brown eyes of Drosophila, coat color in mice, scale color in fish, and plumage pattern in birds. Almost every imaginable heritable variation in size, length, width, or number of some physical aspect of animals has been recorded. This last fact is extremely important for common descent, since the major morphological differences between many species (e.g. species of amphibians, reptiles, mammals, and birds) are simple alterations in size of certain aspects of their respective parahomologous structures.

2.19 Functional change

One of the major differences between organisms is their capacity for various functions. The ability to occupy one niche over another is invariably due to differing functions.

Prediction: Thus, functional change must be extremely important for macroscopic macroevolutionary change.

2.20 Earth’s strange past and the fossil record

A very general conclusion made from the theory of common descent is that life, as a whole, was different in the past. The predicted evolutionary pattern is that the farther back we look back in time, the more different life should appear from the modern biosphere. More recent fossils should be more similar to contemporary life forms than older fossils.

2.21 Stages of Speciation

The most useful definition of species (which does not assume evolution) for sexual metazoans is the Biological Species Concept: species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.

Prediction: If branching of existing species into new species occurred gradually in the past, we should see all possible degrees of speciation or genetic isolation today, ranging from fully interbreeding populations, to partially interbreeding populations, to populations that interbreed with reduced fertility or with complete infertility, to completely genetically isolated populations.

2.22 Speciations

The standard phylogenetic tree illustrates countless speciation events; each common ancestor also represents at least one speciation event. Prediction: Thus we should be able to observe actual speciation, if even only very rarely. Current estimates from the fossil record and measured mutational rates place the time required for full reproductive isolation in the wild at ~3 million years on average. Consequently, observation of speciation in nature should be a possible but rare phenomenon. However, evolutionary rates in laboratory organisms can be much more rapid than rates inferred from the fossil record, so it is still possible that speciation may be observed in common lab organisms.

Confirmation:
Speciation of numerous plants, both angiosperms and ferns (such as hemp nettle, primrose, radish and cabbage, and various fern species) has been seen via hybridization and polyploidization since the early 20th century. Several speciation events in plants have been observed that did not involve hybridization or polyploidization (such as maize and S. malheurensis).

Some of the most studied organisms in all of genetics are the Drosophila species, which are commonly known as fruitflies. Many Drosophila speciation events have been extensively documented since the seventies. Speciation in Drosophila has occurred by spatial separation, by habitat specialization in the same location, by change in courtship behavior, by disruptive natural selection, and by bottlenecking populations (founder-flush experiments), among other mechanisms.

Several speciation events have also been seen in laboratory populations of houseflies, gall former flies, apple maggot flies, flour beetles, Nereis acuminata (a worm), mosquitoes, and various other insects. Green algae and bacteria have been classified as speciated due to change from unicellularity to multicellularity and due to morphological changes from short rods to long rods, all the result of selection pressures.

Speciation has also been observed in mammals. Six instances of speciation in house mice on Madeira within the past 500 years have been the consequence of only geographic isolation, genetic drift, and chromosomal fusions. A single chromosomal fusion is the sole major genomic difference between humans and chimps, and some of these Madeiran mice have survived nine fusions in the past 500 years.

2.24 Morphological rates of change

Prediction: Observed rates of evolutionary change in modern populations must be greater than or equal to rates observed in the fossil record.

2.25 Genetic rates of change

Prediction: Rates of genetic change, as measured by nucleotide substitutions, must also be consistent with the rate required from the time allowed in the fossil record and the sequence differences observed between species.

3. Random Mutation, Natural Selection And Prediction

I think one of the problems – and the reason why people sometimes say that evolution doesn’t make predictions – is that it is impossible to predict in advance exactly what mutation is going to take place and which gene(s) are going to change.

An example – if you put an organism under severe environmental stress – put a few million bacteria on an agar plate filled with a new antibiotic – then you can predict one of two outcomes: either the bacteria will all die or they (at least one to begin with) will adapt to their new environment.

In general, quantitative genetic theory predicts that the response to selection is proportional to the product of the trait’s heritability and the intensity of selection. We can make a few other specific predictions as well – we can predict which genes will not be altered to get this kind of adaptation – because certain genes are critical to keeping the bacteria alive and/or allowing the bacteria to reproduce and mutations in these genes will kill the bacteria or prevent it from reproducing.

We can also predict that the new resistance gene is more likely to be found on a plasmid, if only because we’ve found most other genes for antibiotic resistance on plasmids – an adaptation in an existing antibiotic resistance gene has the best likelihood of success.

Other than that we’re dependent on random mutation, which by it’s very nature defies precise prediction.

Does that mean we can’t predict the outcome? No, just not precisely what the outcome will be.

4. Darwin Again: Natural Selection And Common Descent Together

Darwin noted one way in which natural selection and common descent are evidentially connected:

“… analogical or adaptive characters, although of the utmost importance to the welfare of the being, are almost valueless to the systematist. For animals, belonging to two most distinct lines of descent, may readily become adapted to similar conditions, and thus assume a close external resemblance; but such resemblances will not reveal, will rather tend to conceal their bloodrelationship to their proper lines of descent.”

Darwin’s point is that similarities involving highly adaptive traits are apt to provide misleading information about ancestry; instead, the best evidence of common ancestry comes from neutral or even deleterious features. For example, the torpedo-like shape of dolphins and sharks does not strongly support the hypothesis that they have a common ancestor, since one would expect big aquatic predators to have this shape, even if they originated separately.

The hypothesis of natural selection predicts that heritability will decline in each lineage, but it says nothing about the heritability that each lineage has when it starts evolving. In contrast, the problem becomes more tractable if two species trace back to a common ancestor. The effect of common ancestry is that lineages begin evolving with the same heritability.

The fact of adaptation hinders one’s ability to test hypotheses of common ancestry, but the fact of common ancestry helps one test adaptive hypotheses.

References

  • The common descent section of this article is largely paraphrased (and abbreviated!) from the 29+ Evidences for
  • Macroevolution by Douglas Theobald from talkorigins.

Other references:

  • Cetacean Evolution article by Edward T. Babinski.
  • Common Ancestry and Natural Selection by Sober and Orzack, 2002.
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