29+ Evidences for Macroevolution

The Scientific Case for Common Descent

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Copyright 1999-2012 by Douglas Theobald, Ph.D.
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Introduction

volution, the overarching concept that unifies the biological sciences, in fact
embraces a plurality of theories and hypotheses. In evolutionary debates one is apt to
hear evolution roughly parceled between the terms "microevolution" and
"macroevolution". Microevolution, or change beneath the species level, may be thought
of as relatively small scale change in the functional and genetic constituencies of
populations of organisms. That this occurs and has been observed is generally
undisputed by critics of evolution. What is vigorously challenged, however,
is macroevolution. Macroevolution is evolution on the "grand scale" resulting in the
origin of higher taxa. In evolutionary theory, macroevolution involves common
ancestry, descent with modification, speciation, the genealogical relatedness of all life,
transformation of species, and large scale functional and structural changes of
populations through time, all at or above the species level ( Freeman and Herron
2004; Futuyma 1998; Ridley 1993).

Universal common descent is a general descriptive theory concerning the genetic

origins of living organisms (though not the ultimate origin of life). The theory
specifically postulates that all of the earth's known biota are genealogically related,
much in the same way that siblings or cousins are related to one another. Thus,
universal common ancestry entails the transformation of one species into another and,
consequently, macroevolutionary history and processes involving the origin of higher
taxa. Because it is so well supported scientifically, common descent is often called the
"fact of evolution" by biologists. For these reasons, proponents of special creation are
especially hostile to the macroevolutionary foundation of the biological sciences.

This article directly addresses the scientific evidence in favor of common descent and
macroevolution. This article is specifically intended for those who are scientifically
minded but, for one reason or another, have come to believe that macroevolutionary
theory explains little, makes few or no testable predictions, is unfalsifiable, or has not
been scientifically demonstrated.
Outline

Introduction Part I. A unique, historical phylogene

Universal Common Descent Defined 1. Unity of life

Evidence for Common Descent is Independent of Mechanism 2. Nested hierarchies

What Counts as Scientific Evidence 3. Convergence of independent phylo

o Statistics of incongruent ph
Other Explanations for the Biology
4. Transitional forms
How to Cite This Document
o Reptile-birds
Scientific Evidence and the Scientific Method
o Reptile-mammals
Phylogenetics introduction
o Ape-humans
Figure 1: A consensus universal phylogeny
o Legged whales
Cladistics and phylogenetic reconstruction
o Legged seacows
o Maximum parsimony
5. Chronology of common ancestors
o Maximum likelihood

o Distance matrix methods

Statistical support for phylogenies

Does phylogenetic inference find correct trees?

Caveats with determining phylogenetic trees

Part 3. Evolutionary opportunism Part 4. Molecular evidence

1. Anatomical parahomology 1. Protein functional redundancy

2. Molecular parahomology 2. DNA functional redundancy

3. Anatomical convergence 3. Transposons

4. Molecular convergence 4. Redundant pseudogenes

5. Anatomical suboptimal function 5. Endogenous retroviruses

6. Molecular suboptimal function

What is Universal Common Descent?

niversal common descent is the hypothesis that all known living, terrestrial
organisms are genealogically related. All existing species originated gradually by
biological, reproductive processes on a geological timescale. Modern organisms are the
genetic descendants of one ancient, original species (broadly defined as a communal
population of organisms exchanging genetic material). Genetical "gradualness", a much
misunderstood term, is a mode of biological change that is dependent on population
phenomena; it is not a statement about the rate or tempo of evolution. Truly genetically
gradual events are changes within the range of biological variation expected between
two consecutive generations. Morphological change may appear fast, geologically
speaking, yet still be genetically gradual ( Darwin 1872, pp. 312-317; Dawkins 1996,
p.241; Gould 2002, pp. 150-152; Mayr 1991, pp. 42-47; Rhodes 1983). Though gradualness
is not a mechanism of evolutionary change, it imposes severe constraints on possible
macroevolutionary events. Likewise, the requirement of gradualness necessarily
restricts the possible mechanisms of common descent and adaptation, briefly discussed
below.

Common Descent Can Be Tested Independently of Mechanistic

Theories

In this essay, universal common descent alone is specifically considered and weighed
against the scientific evidence. In general, separate "microevolutionary" theories are left
unaddressed. Microevolutionary theories are gradualistic explanatory mechanisms that
biologists use to account for the origin and evolution of macroevolutionary adaptations
and variation. These mechanisms include such concepts as natural selection, genetic
drift, sexual selection, neutral evolution, and theories of speciation. The fundamentals of
genetics, developmental biology, molecular biology, biochemistry, and geology are
assumed to be fundamentally correctespecially those that do not directly purport to
explain adaptation. However, whether microevolutionary theories are sufficient to
account for macroevolutionary adaptations is a question that is left open.

Therefore, the evidence for common descent discussed here is independent of specific
gradualistic explanatory mechanisms. None of the dozens of predictions directly
address howmacroevolution has occurred, how fins were able to develop into limbs,
how the leopard got its spots, or how the vertebrate eye evolved. None of the evidence
recounted here assumes that natural selection is valid. None of the evidence assumes
that natural selection is sufficient for generating adaptations or the differences between
species and other taxa. Because of this evidentiary independence, the validity of the
macroevolutionary conclusion does not depend on whether natural selection, or the
inheritance of acquired characaters, or a force vitale, or something else is the true
mechanism of adaptive evolutionary change. The scientific case for common descent
stands, regardless.

Furthermore, because it is not part of evolutionary theory, abiogenesis also is not

considered in this discussion of macroevolution: abiogenesis is an independent
hypothesis. In evolutionary theory it is taken as axiomatic that an original self-
replicating life form existed in the distant past, regardless of its origin. All scientific
theories have their respective, specific explanatory domains; no scientific theory
proposes to explain everything. Quantum mechanics does not explain the ultimate
origin of particles and energy, even though nothing in that theory could work without
particles and energy. Neither Newton's theory of universal gravitation nor the general
theory of relativity attempt to explain the origin of matter or gravity, even though both
theories would be meaningless without the a priori existence of gravity and matter.
Similarly, universal common descent is restricted to the biological patterns found in the
Earth's biota; it does not attempt to explain the ultimate origin of life.

What is Meant by "Scientific Evidence" for Common Descent?

Scientific theories are validated by empirical testing against physical observations.

Theories are not judged simply by their logical compatibility with the available data.
Independent empirical testability is the hallmark of sciencein science, an explanation
must not only be compatible with the observed data, it must also be testable. By
"testable" we mean that the hypothesis makes predictions about what observable
evidence would be consistent and what would be incompatible with the hypothesis.
Simple compatibility, in itself, is insufficient as scientific evidence, because all physical
observations are consistent with an infinite number of unscientific conjectures.
Furthermore, a scientific explanation must make risky predictions the predictions
should be necessary if the theory is correct, and few other theories should make the
same necessary predictions.

As a clear example of an untestable, unscientific, hypothesis that is perfectly consistent

with empirical observations, consider solipsism. The so-called hypothesis of solipsism
holds that all of reality is the product of your mind. What experiments could be
performed, what observations could be made, that could demonstrate that solipsism is
wrong? Even though it is logically consistent with the data, solipsism cannot be tested
by independent researchers. Any and all evidence is consistent with solipsism.
Solipsism is unscientific precisely because no possible evidence could stand in
contradiction to its predictions. For those interested, a brief explication of the scientific
method and scientific philosophy has been included, such as what is meant by "scientific
evidence", "falsification", and "testability".

In the following list of evidences, 30 major predictions of the hypothesis of common

descent are enumerated and discussed. Under each point is a demonstration of how the
prediction fares against actual biological testing. Each point lists a few examples of
evolutionary confirmations followed by potential falsifications. Since one fundamental
concept generates all of these predictions, most of them are interrelated. So that the
logic will be easy to follow, related predictions are grouped into five separate
subdivisions. Each subdivision has a paragraph or two introducing the main idea that
unites the various predictions in that section. There are many in-text references given for
each point. As will be seen, universal common descent makes many specific predictions
about what should and what should not be observed in the biological world, and it has
fared very well against empirically-obtained observations from the past 150+ years of
intense scientific investigation.

It must be stressed that this approach to demonstrating the scientific support for
macroevolution is not a circular argument: the truth of macroevolution is not
assumed a priori in this discussion. Simply put, the theory of universal common
descent, combined with modern biological knowledge, is used to deduce predictions.
These predictions are then compared to the real world in order see how the theory fares
in light of the observable evidence. In every example, it is quite possible that the
predictions could be contradicted by the empirical evidence. In fact, if universal
common descent were not accurrate, it is highly probable that these predictions would
fail. These empirically validated predictions present such strong evidence for common
descent for precisely this reason. The few examples given for each prediction are meant
to represent general trends. By no means do I purport to state all predictions or
potential falsifications; there are many more out there for the inquiring soul to uncover.

Are There Other Scientifically Valid Explanations?

The worldwide scientific research community from over the past 150 years has
discovered that no known hypothesis other than universal common descent can account
scientifically for the unity, diversity, and patterns of terrestrial life. This hypothesis has
been verified and corroborated so extensively that it is currently accepted as fact by the
overwhelming majority of professional researchers in the biological and geological
sciences (AAAS 1990; AAAS 2006; GSA 2009; NAS 2005; NCSE 2012; Working Group 2001).
No alternate explanations compete scientifically with common descent, primarily for
four main reasons: (1) so many of the predictions of common descent have been
confirmed from independent areas of science, (2) no significant contradictory evidence
has yet been found, (3) competing possibilities have been contradicted by enormous
amounts of scientific data, and (4) many other explanations are untestable, though they
may be trivially consistent with biological data.

When evaluating the scientific evidence provided in the following pages, please consider
alternate explanations. Most importantly, for each piece of evidence, critically consider
what potential observations, if found, would be incompatible with a given alternate
explanation. If none exist, that alternate explanation is not scientific. As explained
above, a hypothesis that is simply compatible with certain empirical observations
cannot use those observations as supporting scientific evidence.

How to Cite This Document

Many people have asked how to cite this work in formal research papers and academic
articles. This work is an online publication, published by the TalkOrigins Archive.
There are standard academic procedures for citing online publications. For example, if
you last accessed this page on March 12, 2012, and used version 2.89, here is a
reference in formal MLA style:
Theobald,DouglasL."29+EvidencesforMacroevolution:TheScientific
Case for Common Descent."The Talk.Origins Archive. Vers. 2.89. 2012.
Web.12Mar.2012<http://www.talkorigins.org/faqs/comdesc/>

For more information about citing online sources, see the formal style guidelines given
in the book Research and Documentation in the Information Age: Online .

"... there are many reasons why you might not understand [an explanation of a scientific
theory] ... Finally, there is this possibility: after I tell you something, you just can't believe
it. You can't accept it. You don't like it. A little screen comes down and you don't listen
anymore. I'm going to describe to you how Nature is - and if you don't like it, that's going to
get in the way of your understanding it. It's a problem that [scientists] have learned to deal
with: They've learned to realize that whether they like a theory or they don't like a theory
is not the essential question. Rather, it is whether or not the theory gives predictions that
agree with experiment. It is not a question of whether a theory is philosophically delightful,
or easy to understand, or perfectly reasonable from the point of view of common sense. [A
scientific theory] describes Nature as absurd from the point of view of common sense. And
it agrees fully with experiment. So I hope you can accept Nature as She is - absurd.

I'm going to have fun telling you about this absurdity, because I find it delightful. Please
don't turn yourself off because you can't believe Nature is so strange. Just hear me all out,
and I hope you'll be as delighted as I am when we're through. "

- Richard P. Feynman (1918-1988),

from the introductory lecture on quantum mechanics reproduced in QED: The Strange
Theory of Light and Matter (Feynman 1985).

References
American Association for the Advancement of Science (1990) Science for All
Americans. http://www.project2061.org/tools/sfaaol/sfaatoc.htm

American Association for the Advancement of Science (2006) Multiple Resolutions

Regarding Evolution and Creationism. http://archives.aaas.org/docs/resolutions.php?
t_id=54

Darwin, C. (1872) The Origin of Species. Sixth Edition. The Modern Library, New York.

Dawkins, R. (1996) The Blind Watchmaker. New York, Norton.

Feynman, R. P. (1985) QED: The Strange Theory of Light and Matter. Princeton, NJ:
Princeton University Press.

Freeman, S. and Herron, J. C. (2004) Evolutionary analysis Third edition. Upper Saddle River,
NJ: Pearson/Prentice Hall.

Futuyma, D. (1998) Evolutionary Biology. Third edition. Sunderland, MA: Sinauer Associates.

Geological Society of America (2009)

"Evolution." http://www.geosociety.org/positions/position1.htm
Gould, S. J. (2002) The Structure of Evolutionary Theory. Cambridge, MA: Belknap Press of
Harvard University Press.

Mayr, E. (1991) One Long Argument. Cambridge, Harvard University Press.

National Academy of Sciences. (2005) multiple

statements. http://nationalacademies.org/evolution/Statements.html

National Center for Science Education. (2012) "Voices for Evolution: Statements from Scientific
and Scholarly Organizations."
A compilation of statements from 109 of the world's largest and most prestigious societies of
professional research scientists, on the importance of evolutionary theory.
http://ncse.com/media/voices/science

Rhodes, F. H. T. (1983) "Gradualism, punctuated equilibria, and the origin of species." Nature 305:
269-272.

Ridley, M. (1993) Evolution. Boston: Blackwell Scientific.