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Irreducible Complexity Demystified
Posted April 27, 2003
"Evolution is cleverer than you are."
How Does Irreducible Complexity Get Its Charm?
IC, ID, and Creationism
Argument That Irreducible Complexity Cannot Evolve
- How Might Irreducible Complexity Evolve?
- Irreducible Complexity in Nature
A new term, irreducibly complex, (IC) has been introduced into public
discussions of evolution. The term was defined by Michael Behe in 1996 in
his book Darwin's Black Box: The Biochemical Challenge to
Irreducible complexity (also denoted IC) has gained prominence as the
evidence for the intelligent design (ID) movement, which argues that life
is so complicated that it must be the work of an intelligent designer (aka
God) rather than the result of evolution. As you may have heard, the ID
movement wants this taught in public schools as a new scientific theory.
This essay will, I hope, prove helpful to any school teachers, boards of
education, legislators and members of the press who may be wondering about
The argument from IC to ID is simply:
- IC things cannot evolve
- If it can't have evolved it must have been designed
This article just looks at the first part, the argument that
irreducibly complex systems cannot be produced by evolution, either
because they just can't evolve, or because their evolution is so
improbable that the possibility can be ignored.
Let's take a look at the definition of IC, and then see if we can
figure out its relation to evolution, and why scientists are so
unimpressed. Here is the definition, from page 39 (page numbers refer to
Darwin's Black Box unless otherwise noted):
"By irreducibly complex I mean a single system
composed of several well-matched, interacting parts that contribute to
the basic function, wherein the removal of any one of the parts causes
the system to effectively cease functioning." [emphasis in original]
IC is now a single defined term. The new definition, not the
ordinary meaning of the words, is now our guide. IC refers to an organism
doing something (the function) in such a way that the system (that portion
of the organism that directly performs the function) has no more parts
than are strictly necessary.
How do we decide when the term IC applies? Organisms don't come with
parts, functions and systems labeled, nor are 'part', 'system' and
'function' technical terms in biology. They are terms of convenience. We
might say, for instance, that the function of a leg is to walk, and call
legs walking systems. But what are the parts? If we divide a leg into
three major parts, removal of any part results in loss of the function.
Thus legs are IC. On the other hand, if we count each bone as a part then
several parts, even a whole toe, may be removed and we still have a
walking system. We will see later that Behe's treatment of cilia and
flagella follows this pattern.
What about the boundary of the system? This too is up to us. Take the
digestive system for example. We may be interested only in the action of
acids and enzymes in the stomach, or we may include saliva and chewing, or
the lower intestine where some extraction of water and nutrients
As a mental exercise, try before reading on to formulate an argument to
prove that IC systems cannot evolve. IC is supposed to be the biochemical
challenge to evolution, and thus the case when the parts are molecules,
usually proteins, is the important case. So of course there may be multiple copies of a part.
Losing a part means losing all
copies of it, or at least so many that the function is effectively lost.
2. The Argument That Irreducible Complexity Cannot
Behe's argument that IC cannot evolve is central to ID, so it deserves
our attention. His method is to divide evolution into what he calls
'direct', which he defines in a special way, and 'indirect' (everything
else). He finds that direct evolution of IC is logically impossible, and
indirect evolution of IC is too improbable. The argument against 'direct'
evolution of IC is contained in this long sentence right after the
"An irreducibly complex system cannot be produced directly
(that is, by continuously improving the initial function, which
continues to work by the same mechanism) by slight, successive
modifications of a precursor system because any precursor to an
irreducibly complex system that is missing a part is by definition
The last part of the sentence, "...because any precursor to an
irreducibly complex system that is missing a part is by definition
nonfunctional." is why we should agree to the rest of the sentence. There
are some problems:
- The first part of the sentence refers to slight changes.
Removing a whole part is a major change; this is a major
'disconnect' between the parts of Behe's argument.
- It is not true that a precursor missing a part must be
nonfunctional. It need only lack the function we specified. Even a
single protein does something.
- The actual precursor may have had more parts, not fewer.
- If the individual parts evolve, the precursor may have had the same number of parts, not yet codependent. We will learn more about this possibility shortly.
How can one construct a valid argument that IC cannot be produced
directly? ID proponents have not found a way. Yet it's easy (and left as
an exercise for the reader) once you realize that a valid argument from
definitions requires carefully defining the terms so that the argument
becomes a tautology. This may be accomplished by redefining 'direct' or
'IC', or (best, I think) by defining Behe's expression 'be produced' which
he uses in place of 'evolve'.
A precursor to IC lacking a part can have any functions except the
specified one, which brings us to 'indirect' evolution. Consider a cow's
tail. So far as I know, the main thing a cow uses its tail for is to swat
flies. Did tails originally evolve for this function? Hardly. There were
tails before there were flies. Long ago, tails helped early chordates to
swim. Going back still farther, some very early animals started to have
two distinct ends; one end for food intake (with sense organs for locating
food) and the other end for excretions. As a consequence, this back end,
and muscular extensions of it, could also be used to help the animal to
move. This illustrates yet another important facet of evolution: not only
single mutations, but even large organs may begin more or less
accidentally. It also illustrates that biological functions evolve. Indeed organisms and ecosystems evolve. It may not even make sense to expect a precursor to have had the same function.
The long term evolution of most features of life has not been what
Behe, or indeed most people, would call direct. And even short term
evolution can be indirect in Behe's terms. So it is surprising to read, on
page 40, Behe's argument against indirect evolution of IC systems. Here is
the crux of it:
"Even if a system is irreducibly complex (and thus cannot
have been produced directly), however, one can not definitely rule out
the possibility of an indirect, circuitous route. As the complexity of
an interacting system increases, though, the likelihood of such an
indirect route drops precipitously." (page 40)
He simply asserts that evolution of irreducible complexity by an
indirect route is so improbable as to be virtually out of the question,
except in simple cases. He makes no special connection between indirect
evolution and IC. He offers no evidence. He just asserts that it is too
Actually, a more complex system probably has a long evolutionary
history. Since evolution does not aim at anything in advance, the longer
the history, the more circuitous it may be. And his very limited meaning
of 'direct' renders much indirect that is not circuitous at all. Yet he
"An irreducibly complex biological system, if there is such
a thing, would be a powerful challenge to Darwinian evolution." (page
Here's another exercise: before reading on, try to think of ways that
IC systems, including biochemical ones, might evolve after all.
3. How Might Irreducible Complexity Evolve?
How might an IC system evolve? One possibility is that in the past, the
function may have been done with more parts than are strictly necessary.
Then an 'extra' part may be lost, leaving an IC system. Or the parts may
become co-adapted to perform even better, but become unable to perform the
specified function at all without each other. This brings up another
point: the parts themselves evolve. Behe's parts are usually whole
proteins or even larger. A protein is made up of numerous smaller parts
called amino acids, of which twenty different kinds may be used. Evolution
usually changes these one by one. Another important fact is that DNA
evolves. What difference does this make, compared to saying that proteins
evolve? If you think about it, each protein that your body makes is made
at just the right time, in just the right place and in just the right
amount. These details are also coded in your DNA (with timing and quantity
susceptible to outside influences) and so are subject to mutation and
evolution. For our purposes we can refer to this as deployment of parts.
When a protein is deployed out of its usual context, it may be co-opted
for a different function. A fourth noteworthy possibility is that brand
new parts are created. This typically comes from gene duplication, which
is well known in biology. At first the duplicate genes make the same
protein, but these genes may evolve to make slightly different proteins
that depend on each other.
We can summarize these four possibilities this way:
- Previously using more parts than necessary for the function.
- The parts themselves evolve.
- Deployment of parts (gene regulation) evolves.
- New parts are created (gene duplication) and may then evolve.
The first of these only comes up if we are looking for IC. The others
are the major forms of molecular evolution observed by biologists, phrased
in terms of parts. They can lead to new protein functions, sometimes
slowly and sometimes, especially when parts are redeployed, abruptly. Gene duplication and changes in protein deployment may introduce a new protein 'part' into a system. Then the parts may coevolve to do something better, but in a codependent manner so that all are required, without further change in the number of parts. But what happens in nature?
4. Irreducible Complexity in Nature
Can evolution lead to IC or not? It is time to look at living examples
and let nature decide. Behe's most famous example is a mousetrap. But
since a mousetrap is not alive, it doesn't tell us much about whether or
how living IC systems might evolve. How about a flytrap instead?
5. Venus' Flytrap
The Venus' flytrap, Dionaea muscipula, is a small flowering
plant which grows naturally in acidic wetlands in North and South
Carolina. It has a ferocious looking tooth-edged trap for unwary creatures. It
traps and digests insects to make up for the lack of nitrogen in the soils
of its habitat.
Here's how the trap works. When an insect brushes against the trigger
hairs in the center, the lobes snap most of the way shut with surprising
speed. If a small insect is caught, it may escape between the teeth, and
then the trap reopens without fully closing. If a good sized bug is caught
it is digested over the next few days as the trap closes the rest of the
way. Then the trap reopens. A trap can only be fully closed about 4 times,
so it must be used sparingly.
Do we have an IC system here? We must specify a function and all the
parts needed to carry it out (and no extra parts). The function of
interest is trapping insects for food in a manner that brings the plant
more benefit than the cost of the trap. The parts are the two lobes, the
hinge between the lobes (the midrib of the leaf, which anchors the lobes),
the trigger hairs, and spines projecting from the edges of the lobes that
make a set of bars as the trap closes. The system is just all these parts,
and the trap needs all its parts in order to work. Hence it is an IC
How might this trap have evolved? I say 'might' have because Venus'
flytraps haven't left any fossils that I know of, except a few grains of
pollen. Are there any related plants that might provide a clue? Let's look
at the well known sundews (Drosera). Sundews trap insects using
flypaper traps, slowly closing around insects that get stuck. Darwin,
whose book Insectivorous Plants 
is now available online,
made careful observations of these remarkable plants, especially the round
leaf sundew D. rotundifolia. As Darwin notes,
If a small organic or inorganic object be placed on the
glands in the centre of a leaf, these transmit a motor impulse to the
marginal tentacles. The nearer ones are first affected and slowly bend
towards the centre, and then those farther off, until at last all become
closely inflected over the object. This takes place in from one hour to
four or five or more hours. [...] Not only the tentacles, but the blade
of the leaf often, but by no means always, becomes much incurved, when
any strongly exciting substance or fluid is placed on the disc. Drops of
milk and of a solution of nitrate of ammonia or soda are particularly
apt to produce this effect. The blade is thus converted into a little
cup. The manner in which it bends varies greatly. [2,
pp 9, 12]
Here is D. rotundifolia with a fly; Makoto Honda 
shows the action
with a faster species, D. intermedia. Recent genetic research
confirms that Venus's flytrap and the waterwheel plant Aldrovanda
are related and are in the sundew family Droseraceae, and that snap-traps
very likely evolved from flypaper traps 
as Darwin thought:
CONCLUDING REMARKS ON THE DROSERACEAE.
The six known genera composing this family have
now been described in relation to our present subject, as far as my
means have permitted. They all capture insects. This is effected by
Drosophyllum, Roridula, and Byblis, solely by the viscid fluid
secreted from their glands; by Drosera, through the same means,
together with the movements of the tentacles; by Dionaea and
Aldrovanda, through the closing of the blades of the leaf. In these
two last genera rapid movement makes up for the loss of viscid
secretion. [...] The parent form of Dionaea and Aldrovanda seems to
have been closely allied to Drosera, and to have had rounded leaves,
supported on distinct footstalks, and furnished with tentacles all
round the circumference, with other tentacles and sessile glands on
the upper surface. [2,
pp 355-6, 360].
How did the Venus' flytrap avoid the argument that IC can't evolve? In
two ways. First, rather than gaining a part, it lost a part - the glue
that the sundews use. Even more interestingly, the trap was able to evolve
because the parts evolved. The trap started out as a Drosera-like
leaf, and the parts of the leaf were progressively changed. This makes a
striking contrast with the mousetrap which Behe has repeatedly presented
to illustrate why IC cannot evolve. As a manufactured item the mousetrap
neatly illustrates his definition, but with its static parts it cannot
model evolution. With evolving parts, nature can create a snap-trap after
all. The mechanical and manufacturing analogies so influential in Behe's
thinking miss the flexibility of living things.
6. How to Eat Pentachlorophenol
Pentachlorophenol (PCP) is a highly toxic chemical, not known to occur
naturally, that has been used as a wood preservative since the 1930's. It
is now recognized as a dangerous pollutant that we need to dispose of. But
Evolution to the rescue! A few soil bacteria have already worked out a
way to break it down and even eat it. And conveniently for us, they do it
in an irreducibly complex way. The best known of these bacteria is called
Sphingomonas chlorophenolica (also called Sphingobium
The PCP molecule is a six carbon ring with five chlorine atoms and one
hydroxyl (OH) group attached. The chlorines and the ring structure are
both problems for bacteria. S. chlorophenolica uses three enzymes
in succession to break it down, as follows: the first one replaces one
chlorine with OH. The resulting compound is toxic, but not quite as bad as
PCP itself. The second enzyme is able to act on this compound to replace
two chlorines, one after the other, with hydrogen atoms. The resulting
compound, while still bad, is much easier to deal with, and the third
enzyme is able to break the ring open. At this point, what is left of PCP
is well on its way to being food for the bacterium.
All three enzymes are required, so we have IC. How could this IC system have evolved? First of all, bacteria of this
type could already metabolize some milder chlorophenols which occur
naturally in small amounts. In fact the first and third enzymes were used
for this. As a result the cell is triggered to produce them in the
presence of chlorophenols. The second enzyme (called PcpC) is the most
interesting one; the cell produces it in sufficient quantity to be
effective all the time instead of just when it is needed in its
normal metabolic role. Thanks to this unusual situation PcpC is available
when it is needed to help eat PCP.
The inefficient regulation of PcpC is evidently the key to the whole
process. So far as biologists can tell, a recent mutation that changed the
deployment of this enzyme is what made PCP degradation possible for this
bacterium. It also happens that both PcpC and the first enzyme in the
process are now slightly optimized for dealing with PCP; they handle it
better than the corresponding enzymes in strains of S.
chlorophenolica that use PcpC only in its normal role, but not nearly
as well as would be expected for an old, well adapted system. These
factors, combined with the fact that PCP is not known to occur naturally,
make a strong circumstantial case that this system has evolved very
The chemistry and probable evolution of this system are explained in
much greater detail in Shelly Copley's article "Evolution of a metabolic
pathway for degradation of a toxic xenobiotic: the patchwork approach" in
Trends in Biochemical Sciences .
7. Hemoglobin for the Active Life
Hemoglobin is a wonderful protein that picks up oxygen in our lungs and
delivers it to the rest of our cells. Oxygen binds to hemoglobin very
quickly in our lungs and stays bound. Then in our tissues oxygen is
released very quickly. How does this happen? What we call a hemoglobin
molecule is a complex of four hemoglobin chains, or subunits. There are
two each of two different chains called alpha and beta hemoglobin. The
complex binds reversibly to oxygen, one O2 molecule per each
subunit. It tends not to bind to the first oxygen until the oxygen
concentration is fairly high, which is the usual situation in our lungs.
Then the complex changes shape so that the next O2 binds more
readily, the third still faster, and the fourth faster yet. Then it holds
the oxygen until the surrounding oxygen concentration is quite low, which
happens in our tissues. When finally one oxygen is released, the next is
released faster and so on. This mechanism for oxygen transport is much
more efficient than can be achieved with alpha or beta hemoglobin alone,
and allows for our active life style. It takes all four parts to do this;
take away part of the complex and it doesn't work .
So we have another IC system. Behe discusses hemoglobin briefly (pp
206-207), mainly commenting that it makes a poor case for Design. He
doesn't mention that it is IC. This talk.origins post 
has some sharp commentary on the subject.
The hemoglobins (globular proteins incorporating a heme group, which in
turn cradles an atom of iron) turn out to be a widespread protein family
with a long history. They occur in plants and bacteria as well as in
animals, and have diverse functions including oxygen transport, oxygen
storage, scavenging oxygen to protect some metabolic processes from it,
and electron transfer. Interestingly, these diverse functions depend
critically on when and where the protein is deployed. Commenting on this
in his article "The Evolution of Hemoglobin", Ross Hardison says "This
suggests that the creation of new protein functions arises as much from
changes in regulation as from changes in structure." [8,
p 126]. Fetal hemoglobin, which must extract oxygen from the mother's
hemoglobin, is a good example of this. We always have the genes for it,
but only make it at the right time. Gene duplication has also played a key
role. Lampreys and hagfish, which don't have jaws, also don't have the
alpha and beta varieties of hemoglobin. Instead they have just one variety
of hemoglobin in their blood, and not so efficient oxygen transport. The
gene duplication which led, after further changes, to our distinct alpha
and beta chains evidently happened in the ancestor of all living
vertebrates with jaws.
Let's take stock of what we have learned before moving
on to more complicated examples. Venus' flytrap makes an instructive
comparison with Behe's mousetrap. In one, the parts evolve. In the other,
they don't. What a difference this detail makes. The protein parts of
biochemical systems also evolve, so the flytrap is a good model for them
and the mousetrap isn't. The flytrap and hemoglobin show in different ways
that removing a part is often not the same as evolution in reverse. The
flytrap has already lost a part (the glue that Drosera use to trap
insects). With hemoglobin, taking away either the alpha or the beta chain
would be a disaster unless the whole animal could be 'evolved back' to a
much earlier stage.
Both hemoglobin and the recent evolution of a way to metabolize PCP
show that what we have called 'deployment of parts' is important in
evolution. Biologists usually call this regulation of gene expression, or
just gene regulation. From another point of view, it is called co-option
or recruitment of a protein to a new function. If a protein takes on two
roles, any subsequent duplication of the corresponding gene will be
subject to selection for both its regulation and the separate functions.
Hence this duplication will be more likely to persist and spread in the
Here's another interesting thing about the PCP example: it amounts to
'adding a part to a previously non-functional system', which is exactly
what Behe thinks cannot happen, because he thinks the organism couldn't
have lived without that part. It turns out that a single mutation can
create a new function and mechanism, allowing the organism to live better
or in a new environment. This is indirect evolution in Behe's terms, but
to DNA it is just another mutation.
So far IC seems to be no problem for evolution. Is there anything to
the biochemical challenge? Let's look at the impressively complicated
examples on which IC's reputation rests.
8. The Blood Clotting System: is it IC?
Blood clotting is an example of what biochemists call a cascade: one
protein does something, which starts another protein doing something,
which starts another.... Cascades, and the clotting cascade in particular,
are among the favorite examples of ID proponents. Yet giving a precise
specification of system, parts, and function so that the specified system
is IC turns out to be difficult. Hard to specify or not, it is still one
of Behe's favorite examples. He devotes his entire fourth chapter to it.
After explaining how it works, he indicates that scientists know almost
nothing about how it evolved. His main evidence for this is a nontechnical
lecture given by Russell Doolittle. But of course that talk, using
analogies to Yin and Yang, was not meant to convey a technical
understanding. After several people commented on this, Behe responded with
an online essay "In Defense of the Irreducibility of the Clotting Cascade"
The defense comes down to saying that evolution of this system would
require too many 'unselected steps'. But this is not true, as pointed out
by Ken Miller in Finding Darwin's God 
and in his online article 
where he gives more details than the publisher wanted in the book.
The clotting cascade is a member of a family of cascades with a long
pedigree. Our immune system includes a related cascade which Behe
considers to be IC, but see Matt Inlay's article "Evolving
A recent paper by Krem and Di Cera (13)
pursues the evolution of cascades farther down the evolutionary tree. They
discuss biochemically similar cascades in horseshoe crabs, fruit flies,
and ourselves. They find that "Extensive similarities suggest that these
cascades were built by adding enzymes from the bottom of the cascade up
and from similar macromolecular building blocks." Behe argues that this
type of evolution would not happen because there would be unselected
steps. But he thinks in terms of precursor systems with missing parts, not
in terms of ancestor organisms in different environments with different
problems to solve. This may reflect a difference between thinking like a
chemist and thinking like a biologist. Early forms of the cascade occurred
in animals without a high pressure circulatory system like ours. In
horseshoe crabs, for instance, a simpler form of the clotting cascade
serves to entangle invading bacteria. There is no reason to presume
unselected steps (other than gene duplication, which may be neutral at
first) if the organism and its way of living and its environment are
But have you noticed something missing from our discussion of the
clotting cascade? We haven't proven that it is IC. The way to do this, as
Behe tells us on page 42, would be to take the parts one by one and show
that each is required for clotting. Or point to published research that
does this. Surely Behe took care of this detail in the fourth chapter of
his book? No. He 'proved' it rhetorically, but not systematically. Well
then, when he published a web page several years later entitled "In
Defense of the Irreducibility of the Blood Clotting Cascade" 
he must have filled in the details? No again. He advanced his argument
against the evolvability of the clotting cascade, but that has been
Meanwhile, the little matter of proving that it is IC has been overlooked.
And there is evidence to the contrary: whales, mammals like us, lack a key
part called Hageman factor but their blood clots anyway .
Under questioning at a recent meeting 
Behe finally agreed that the cascade is not IC after all. Indeed, Acton
gives reasons why he never should have thought so .
(As far as I know, Behe has not 'done his homework' on any of his examples
except the mousetrap).
9. Swimming Systems
We come now to what have become the very most important purported
examples of IC in nature: swimming systems. These are flexible projections
that microbes use to move themselves through fluids. The three main types
of microbes, bacteria, archaea, and single celled eukaryotes, use
different swimming structures, and there are major differences between
species of each type. Some bacteria even manage to swim without flagella,
including little understood Synechococcus 
and much better understood Spiroplasma melliferum .
Of course microbial motion is not limited to swimming. They also have ways
to move along surfaces and maneuver in sand and ooze. Bardy et al. review
almost all of the known ways bacteria and archaea move .
Swimming systems depend on what are called molecular motors, a favorite
topic of molecular biologists. Those who are curious about molecular
motors may start here .
Brownian ratchets, fascinating in their own right ,
are one of the energy sources for these tiny motors.
From a biological perspective, the function of an organism is to live
and grow enough to reproduce. The function of any part of the organism is
to contribute to this in any ways whatsoever. Appendages can help a cell
in various ways such as sensing the environment, finding food or mates or
communicating with other cells. It helps if the appendage can move about.
This in turn will move the cell a little. (Think of waving your arm under
water). In an environment where swimming is advantageous, it is not
surprising that the ability to swim would evolve. Never the less, as the
evolution of vertebrate systems like the clotting cascade and the immune
system has become better understood, ID proponents have come to rely more
and more on swimming systems, especially the bacterial flagellum, as the
real evidence for Design in nature.
10. The Eukaryote Cilium
Eukaryotes are any organisms like trees, people, protozoa and amoebae
which, unlike bacteria, have their DNA in a separate nucleus within the
cell. Many eukaryote microbes propel themselves through water by waving
projections called cilia, which they also use to collect food such as
bacteria. A bit of terminology: cilia are also called flagella, especially
when a cell only has one or two. The microbes are then called flagellates.
But eukaryote flagella and bacterial flagella are entirely different
How do we define an IC system in the case of the eukaryotic cilium?
Behe first specifies the system as the entire cilium. The function of the
system is to move the cell through liquid by a sort of waving action. What
about parts? At the level of biochemical machines, one usually thinks of
individual proteins as parts. But Behe simply divides a cilium into three
large parts, which he calls 'motor, connector, and paddle' (page 65). It
is clear that a cilium wouldn't work without each of these big parts, so
we have IC. Cilia are many and diverse (for examples see Finding
Darwin's God [10,
page 142]) and may contain two hundred or so different proteins and
various numbers of microtubules. Some proteins are always present; others
vary from microbe to microbe. If we take proteins as our parts (the
biochemical challenge), then cilia aren't IC; no one has been able to find
a real cilium with an 'irreducible' set of proteins. If we take
microtubules as our parts as Miller does, the cilium is not IC. But with
Behe's parts it is IC. Remember, it's up to us to choose function, system
and parts to satisfy the definition. Or not. So it turns out that being IC
or not is not a property of the cilium itself. It depends on choices we
With the parts (motor, connector and paddle) so removed from the
mutation-by-mutation level of change, how does Behe relate the ICness of
the system to its evolution? First, with his choice of function, parts and
system, it is IC. This rules out 'direct' evolution to his satisfaction.
What about 'indirect', i.e. normal evolution, taking into account that
everything changes including functions? This is ridiculed on pages 65-67. Although the cilium is an
extension of the cell's cytoskeleton, he suggests that a proto-cilium
would be disadvantageous. He winds up:
"... but even if [a proto-cilium] were at the cell surface,
the number of motor proteins would probably not be enough to move the
cilium. And even if the cilium moved, an awkward stroke would not
necessarily move the cell. And if the cell did move, it would be an
unregulated motion using energy and not corresponding to any need of the
So a proto-cilium would be useless and probably even a harmful waste of
resources until it was perfected, in Behe's opinion.
Microbes do not agree, and make use of a variety of projections that
have the 'defects' that Behe mentions. The amoeba Raphidiophrys
pallida, shown here )
has projections called axopodia which it uses to capture prey and to move
itself along a surface such as a bit of pond weed. The protozoan
Actinophrys in this Pond Scum Action Video 
explores with gently waving axopodia. Foraminifera are very common
protists in the oceans and in the ooze beneath. They use projections
called reticulopodia to find and capture food, and to maneuver among sand
These projections, although dependent on many of the same proteins for
motion, are not cilia. But they resemble the clumsy cilia that Behe
objects to, and show that his objections do not hold up in nature.
Now, what about cilia in the strict sense? The cilium in its early form
would have been too short to function as a rowing device. What could it
have done? The first flagellates are long gone, but we can still learn
from the ones at the base of the family tree as it now exists. The soil
dwelling flagellate Phalansterium is about as basal as any. It is
hard to watch in action, but it probably uses its cilium to sense the
environment and to collect bacteria to eat. The eukaryote family tree has
two main branches, leading to plants and animals. At the base of these
branches we find water dwelling flagellates that push water in opposite
Mastigamoeba creep along surfaces and move their cilium to create a
slight current toward themselves, drawing in food particles.
Choanoflagellates, on the line leading to animals, use their cilium to
push water away .
This draws in more water, and food along with it.
Any projection that could stir the water at all would help to bring
more food to the microbe. Gradually improving it naturally leads to a
swimming system. Behe's objections overlook evolutionary change of
function, which would naturally occur to a biologist but perhaps not to a
chemist like him.
11. The Archaeal Flagellum
Archaebacteria, or Archaea for short, have recently been recognized as
an important group of microbes distinct from bacteria and from eukaryotes.
Their flagellum is analogous to a bacterial flagellum, but simpler and
quite different in detail. As the diagram
shows, it resembles another kind of projection called a type IV pilus, to
which it is probably related .
Type IV pili themselves are not used for swimming, but bacteria use them
for simpler ways of moving called twitching and social gliding [19,
Behe has not discussed archaeal flagella, and I am not sure how he would
divide them into parts. They don't appear to fit his preferred three part
division (a motor, then a rotor or connector, then a third part which
pushes against the medium) on which he bases his statement that "the
complexity is inherent in the task itself" (page 65).
12. The Bacterial Flagellum
Here it is -- the number one argument for design in nature. ID
advocates have even made a movie called Bacterial Flagella: A Paradigm for
Design. It is on sale at the ARN web site 
and briefly discussed in talk.origins .
Behe said recently:
"If [biologist Jerry] Coyne demonstrated that the
[bacterial] flagellum, (which requires approximately forty gene
products) could be produced by selection, I would be rather foolish to
then assert that the blood clotting system (which consists of about
twenty proteins) required intelligent design". 
Bacterial flagella are many, diverse, and complicated. Behe concludes
that any bacterial flagellum is composed of at least three parts: a
paddle, a rotor, and a motor, and so with swimming as the specified
function must be IC (page 72). Even at this crude level, the ICness of a
flagellum is not so clear. The problem is that there are additional parts
to a complete flagellum. For instance, there are proteins at the base that
react to external stimuli and turn the motor on and off, and in some
flagella cause it to change directions. And there are other proteins that
are arranged in rings where the flagellum passes through the cell
But the more interesting question is: could a flagellum be IC with
proteins, not paddles etc. as parts? Remember, IC is supposed to be the biochemical
challenge to evolution. We've already seen that it isn't such a challenge
after all, but so much has been made of the purported ICness of the
flagellum that one should be well informed on the subject just to be more
interesting at parties :). In order to decide, one must first choose a
flagellum. Even within a single bacteria species, different strains may
have different proteins and different numbers of proteins in their
flagella. Even a single rod-shaped bacterium may have quite different
flagella at its ends and around its sides. Next, discover and list all the
proteins in that particular flagellum. This requires deciding just where
it begins, and one's decision about this may depend on the exact function
one has in mind for 'the' flagellum. Then comes the hard part: proving
that every last protein is required for the function. Oddly, ID proponents
show no interest in doing any of this work, not even picking a particular
flagellum of a particular bacterium to start on. It is as if just
asserting the ICness of 'the' flagellum gives them full satisfaction.
What's the answer? Is any flagellum IC with proteins as parts or not?
As this would depend on some arbitrary criteria, scientists have not
pursued this question as such. But quite a bit has been learned about
various flagella. It is clear that all of them absolutely require a good
many of their proteins in order to function as swimming systems. But not
one is yet known to require every last protein, and some are known not to
Could a flagellum be IC with proteins as parts? Sure. As we have seen in
the much simpler case of hemoglobin, proteins can evolve to become
codependent. There may be a perfectly IC flagellum out there just waiting
to be discovered.
Even so, it wouldn't be the simplest swimming system. As
shows, a bacterial flagellum is much more complex than an archaeal one.
This is in part because it is built from, in fact secreted by what is
called a type three secretion system (TTSS). This is a complicated thing
in itself. It is a tiny tube which starts below the cell wall and sticks
out through it, and serves as a conduit for protein export. The flagellar
TTSS (there are other kinds) specializes in secreting the rest of a
flagellum. The TTSS base counts as part of the flagellum, and is itself
about as complex as an archaeal flagellum.
Since it is more complicated than is required for swimming alone, you
might suspect that a bacterial flagellum has other functions. You would be
right. These other functions vary from bacterium to bacterium and from
situation to situation, and scientists have only recently been able to
observe them. First, some flagella also export proteins, including ones
that cause sickness .
This is not too surprising since that's what the other TTSS's are known
But spirochetes, the spiral shaped bacteria, use flagella in a way one
wouldn't expect. Their flagella don't stick out, yet are used for
swimming, burrowing, and maintaining the cell's shape. Flagella are grown
at both ends and extend toward the middle under the outer membrane.
The flagella maintain the cell's spiral shape, and by rotating can create
a moving wave along the cell, causing the cell to move in the opposite
It is not easy to observe the behavior of individual bacteria in the
wild. Just recently though, Danish researchers noticed some unusual
behavior by bacteria living on low oxygen marine sediments. To see exactly
what the bacteria were doing, they recreated the ecosystem in the
laboratory. Who would have thought that some bacteria, shaped like
slightly bowed rods, would tether themselves to the sediment with a mucus
stalk secreted from the center and then use flagella at both ends to move
like a propeller? But that's what these bacteria do. They create a tiny
current, refreshing the water around them much faster than diffusion alone
could do it .
Bacteria can move across surfaces in organized swarms, and quickly
colonize a new food source such as your own much larger cells. When
swarming, they often grow many more flagella than usual and make
cell-to-cell contacts with these flagella .
Some bacteria also use their flagella to hang on to our cells as they try
to break in and eat the cell contents .
This brings us to the dark side of design. Flagella participate in the
cause of quite a few bacterial diseases, including diarrhea ,
ulcers and urinary tract infections .
If the Designer is directly responsible for flagella then he is implicated
as a cause of human diseases. Diarrhea is no joke; it is a leading cause
of infant death in some parts of the world. To make matters worse, one can
hardly give the Designer credit for flagella without also crediting him
with TTSS's in general .
This puts the Designer solidly behind Bubonic plague [41,
and many other diseases .
Happily, science makes such beliefs unnecessary. Swimming
systems provide a good illustration of how (not) to think about
evolution. Behe argues that evolution can't produce them because they are
IC (a dubious claim and not an obstacle to evolution as we have seen). He
buttresses this by arguing that is quite improbable that a swimming system
good enough to be useful would appear all at once. And it wouldn't evolve
slowly, he supposes, because until it became an effective system, there
would be nothing for natural selection to select. However, he envisions a
part that sticks out, but that has no use at all other than swimming - and
at first it can't even do that. But parts that stick out have a number of
functions, and bacterial flagella clearly have several. If there is another
reason for it to be there, the sticking out part can gradually evolve more
abilities. This involves change of function, or indirect
evolution as Behe calls it. He dismissed this possibility, saying that it
is improbable. A closer look shows the opposite.
13. IC Cores
Have you noticed that none of our complex examples is IC at the
molecular level? The argument that IC can't evolve is made in general
terms, but it is at the molecular level that the 'biochemical challenge to
evolution' is supposed to really count. Granted, we have seen that IC can
evolve, but proponents of 'IC implies ID' are able to overlook this. They
have not entirely overlooked the fact that not even one impressively
complicated molecular system has been shown to be IC. The proposed
solution to this problem is that these systems have 'IC cores': if you
remove proteins one by one, at some point what is left will be IC. And if
you remove parts in a different order, you may find other IC cores. But
arbitrarily removing parts that have become coadapted is not "evolution in
reverse", so IC cores don't tell us about evolution. And how are they
relevant to IC if nature uses more than the core? All I know is that IC
cores seem to matter to ID proponents.
Now let's take a more biological look at it. The whole irreducible
complexity argument is based on fixed functions, parts, systems,
organisms and environments. In nature all these things vary. Evolution,
appropriately enough, is all about change. The search for what might be
called an evolutionarily irreducible core to any of the complex examples
will take you back, back, back to who knows what? The immediate precursor
may have had more parts. Or if it had fewer parts, it is probably not
appropriate to remove a part before modifying the parts so that they are
not coadapted and codependent. Perhaps the whole organism should be
modified and placed in a different environment before removing a part.
Where do you stop ?
Since we found that simple IC systems readily evolve, why are
complicated ones hard to find? Some of the same modes of change that can
produce IC can just as well add complications that don't fit the
definition. Most genes are members of gene families that have grown
through gene duplication over time. The time since a particular
duplication happened can be estimated by the amount of difference between
members of the family. This is a dead giveaway that the organism's
ancestors got along with fewer "parts". And given a large number of parts,
these parts are likely to have additional functions, which is a good
reason for there to be more parts than the minimum needed for what we
decide is 'the' function of those parts. For example, we noted earlier
that whales lack one of our blood clotting proteins, called Hageman
factor. People are sometimes born with a mutation that leaves them with
only 40 to 60 percent of the normal amount of Hageman factor. Their blood
still clots. But women with reduced Hageman factor tend to have more
14. How Does Irreducible Complexity Get Its Charm?
Evolution doesn't even notice whether a combination of parts, system
and function chosen by an observer happens to satisfy a definition in a
book. It just doesn't matter. This is in a nutshell what scientists have
been saying since Darwin's Black Box was published .
Yet the book has been very influential with the public (see for instance
the 370 or so reviews at amazon.com ).
And it provides the one seemingly scientific reason to teach ID in public
school science classes.
How can the book's success with laymen be explained? First, it appears
that evolution is hardly taught in the US. Basic knowledge such as the
four modes of evolutionary change given at the beginning of this essay
would show a reader that evolution is much too flexible for IC to be an
issue. Biological basics and careful reading would enable one to see that
Behe's theoretical argument that IC can't evolve is unsound.
Without a good basic understanding of biology, a tricky ambiguity sets
in. First, there is the definition of IC. Then comes the apparent proof
that it cannot evolve. After that, 'unevolvable' is casually used as the
meaning of IC. To complete the picture, the subtext all along is that IC
is impressively complicated. Thus one's attention is directed away from
simple cases which directly show how basic modes of evolutionary change
may lead to IC. The definition is used to argue that IC exists, and the
other two meanings seal the conviction that IC systems are very unnatural
indeed. It is a case of using words which seem to mean what some people
want them to mean, but on closer examination don't. This results in the
reader losing sight of the fact that none of Behe's examples are in fact
IC in biochemical terms, and of the fact that IC doesn't matter for
evolution in any case, so that there actually is no 'biochemical challenge
to evolution' at all.
15. IC, ID, and Creationism
Is IC/ID a form of creationism? It looks like it to many people, but
proponents reject that label. Let's see if we can sort it out.
You may have heard that ID differs from creationism in not insisting
that the earth is only a few thousand years old. It's not quite that
simple. Creationists come in both 'young earth' and 'old earth' varieties.
So do ID proponents. The difference is that old and young earth
creationists are at odds. ID, on the other hand, takes a 'big tent'
approach. You are free to accept geological evidence or wave it aside. The
Designer could have made the earth look older than it is.
ID mirrors creationist thinking in a fundamental way that you might not
notice if you are not familiar with the genre. All creationists agree that
there are some inherited genetic changes. The different breeds of dogs,
for instance, are not held to be special creations. But creationists
always divide evolutionary changes into two kinds: there is a simple kind
of change, which they agree evolution can do. But evolution is always
somehow blocked from causing the really significant changes, either
because evolution just can't do it, or it is so improbable that you can
forget about it in practice. Is this beginning to sound familiar?
IC biochemical systems are what biochemist Behe has decided evolution
cannot produce. According to him, they literally can't evolve directly and
their indirect evolution is too improbable.
Creationists often assert that intermediate forms along the way to
things they say could not evolve just would not work, and make fun of
intermediates (as described by themselves). As we have seen,
Behe also does this. In support of this view, he proposes what he calls
minimal function as "... another difficulty for Darwin" (page 45). This is
explained by imagining being stranded in the middle of a lake in a small
boat powered by a propeller that only turns at one revolution per hour.
The implication is that a flagellum must have been a quite capable
swimming system the first time out, or it couldn't evolve. This idea is
another consequence of dismissing change of function, or indirect
evolution as he calls it, out of hand. As we already know, parts that
stick out, including flagella as the finely adapted swimming organs that
they now are, can have other functions. The projection that became the
flagellum as we know it may not have have started as a swimming system at
all, and is very unlikely to have had that function alone.
Precisely pinpointing a barrier that evolution can't cross is the Holy
Grail of creationism. Behe claims to have done it. Naturally creationists
are enthusiastic, nor is it surprising that many observers see IC and ID
as simply a new version of creationism. Still, leading proponents try to
distance themselves from the term. The term 'neocreationism' is a good
compromise. It acknowledges new developments and important continuities
Why are biologists never convinced that the barriers claimed by
creationists are real? It always comes down to the same things: Given a
population with inherited variation and also new variations from mutation
or immigration, evolution occurs. Natural selection (instead of only
random drift) occurs if some heritable variations are related to
reproductive success. This process takes no notice of whether the changes
that occur are direct or not, or whether something is becoming IC.
Likewise, evolution just doesn't notice the other barriers proposed by
There is one difference that may be of interest to school boards. In
the past, creationists have, naturally enough, formed creationist
organizations such as the venerable Institute for Creation Research and
the net-based Answers in Genesis. The leaders of the ID movement on the
other hand are all high ranking members of a political organization
calling itself the Discovery Institute .
Irreducible complexity, intelligent design's closest brush with
biology, is marked by three ironies.
- IC is supposed to be important because it cannot evolve. But it can
evolve, in the same ways that anything else does.
- Not one of the impressively complex biochemical systems said to be
IC by IC/ID proponents has been shown to be in fact IC and several are
known not to be. The known cases of IC are simpler and their evolution is
- Although the subject is religiously motivated, proponents have
focused on bacterial flagella as the last hope for a highly complex IC
system. This has the unintended consequence of making The Designer (aka
God) responsible for serious diseases.
It is easy to see why scientists are not impressed by the claim that IC
cannot evolve. IC is a matter of an observer specifying a combination of function, parts and system so that the specified function requires all the parts. There is no way for evolution to be sensitive to this, no way for it to matter at all. Nor does nature care about 'direct' vs 'indirect' evolution as perceived by us. Indirect evolution is as normal as tails on cows. Evolution merely requires populations with heritable
variation. The processes of mutation, natural selection and random drift
are not sensitive to whether a change will be deemed direct or not, nor
whether a function, system and parts as specified by some observer are
changing to meet the 'all parts required' condition.
There was supposed to be a special reason why it was impossible or at least very difficult for evolution to arrive at an 'all parts required' situation, but there is no such reason. The proposed reason was based on overlooking standard evolutionary processes and making analogies to manufactured items. Comparing Behe's mousetrap to Venus' flytrap confirms the reasonable suspicion that analogies and arguments based on manufactured items lead to underestimating nature. Since IC can occur in the ordinary course of events we have a known process, evolution, which is acting in the present and which given time is sufficient to produce the adaptations that Behe finds perplexing. This is like the raising of the Rocky Mountains; a known process acting in the present is sufficient, given time, to produce the result. Of course there is no way to predict all the details in either case, nor is it necessary.
Finally, this version of 'gap theology', basing the Designer on gaps or purported gaps in our knowledge (which is not mainstream religion), ends up implicating the Designer in human disease. This makes ID rather questionable as a public school lesson. Gap theology is bad enough at best, and always has the problem that the gaps keep getting smaller. This new version of it is especially bad. Darwin did theologians a favor by freeing them from this sort of thing.
Despite all this, there is a strong political drive to force public
schools to misrepresent neocreationism as science. But misrepresentation
is not acceptable. And it would be awkward to tell teachers to teach ID
science when there isn't any. If it becomes politically necessary to teach
something about the subject, the present essay contains material for
several lessons. And if the plan is to teach 'the controversy', it would
be proper to tell the students that there is no scientific controversy,
although there is a public one. Books like Darwin's Black Box: The
Biochemical Challenge to Evolution are surely part of the reason.
Yet the widespread public acceptance of Behe's thesis is stark evidence that we need stronger science education, especially about evolution.
I thank Victor Eijkhout, Matt Inlay, Ian Musgrave and especially Nick
Matzke, along with the talkdesign crew for helpful discussions. Special
thanks to Barry Rice, author of www.sarracenia.com for permission to use
photos of Venus' flytrap and sundews.
 Behe MJ. Darwin's Black Box: The Biochemical
Challenge to Evolution (New York: The Free Press, 1996).
 Darwin, Charles. Insectivorous Plants
(New York: D. Appleton & Co., 1875. [first published London:
John Murray, 1875]) Insectivorous
 Honda M. (2001). Insectivorous Plants in the
Wilderness. Makoto Honda's carnivorous plants web site.
 Cameron KM, Wurdack KJ, Jobson RW. (2002). Molecular
evidence for the common origin of snap-traps among carnivorous plants.
American Journal of Botany 89:1503-1509.
 Copley SD. (2000). Evolution of a metabolic pathway
for degradation of a toxic xenobiotic: the patchwork approach. Trends in
Biochemical Sciences, 25(6):261-265.
 Ackers GK, Doyle ML, Myers D, Daugherty MA. (1992).
Molecular Code for Cooperativity in Hemoglobin. Science 255:54-63.
 Hines W. (2002). Hemoglobin
and Irreducible Complexity. Talk.origins post.
 Hardison R. (1999). The Evolution of Hemoglobin.
American Scientist 87(2) 126-137.
-- (1998). Hemoglobin from bacteria to man: Evolution of different patterns
of gene expression. Journal of Experimental Biology 201:1099-1117.
 Behe M. (2000). In
Defense of the Irreducibility of the Blood Clotting Cascade: Response
Doolittle, Ken Miller and Keith Robison
Doolittle's article is one of several responses to Orr's review of
Darwin's Black Box, published in the December 1996/ January 1997
issue of Boston Review. The responses including Behe's were published in
the February/March 1997 issue of Boston Review and are online here.
 Miller K. Finding Darwin's God: A Scientist's
Search for Common Ground Between God and Evolution
 Miller K. (2000). The
Evolution of Vertebrate Blood Clotting.
 Inlay M. (2002). Evolving Immunity: A Response to
Chapter 6 of Darwin's Black Box.
 Krem MM, Di Cera E. (2002). Evolution of enzyme
cascades from embryonic development to blood coagulation. Trends in
Biochemical Sciences 27(2):67-74.
 Acton G. (1997). Behe and
the Blood Clotting Cascade. Talk Origins Post of the Month: February
 Semba U, Shibuya Y, Okabe H, Yamamoto T. (1998).
Whale Hageman Factor (Factor XII); Prevented Production Due to Pseudogene
Conversion. Thrombosis Research 90(1):31-37
questions Behe at the Question and Answer session at the American
Museum of Natural History meeting, April 23, 2002.
 Samuel AD, Petersen JD, Reese TS. (2001). Envelope
structure of Synechococcus sp.WH8113, a nonflagellated swimming
cyanobacterium. BMC Microbiol 1(1):4, online here.
 Trachtenberg S, Gilad R, Geffen N. (2003). The
bacterial linear motor of Spiroplasma melliferum BC3: from single
molecules to swimming cells. Molecular Microbiology 47(3):671-697.
 Bardy SL, Ng SYM, Jarrell KF. (2003). Prokaryotic
motility structures. Microbiology 149:295-304.
 Molecular motors:
References for a course on molecular motors at Berkeley.
pallida. Note the axopodia in the second micrograph.
Scum Action Video. An Actinophrys explores its world with
gently waving axopodia.
 Cavalier-Smith T. (2002). The phagotrophic origin
of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst.
Evol. Microbiol. 52:297-354.
 Stechmann A and Cavalier-Smith T. (2002). Rooting
the Eukaryote Tree by Using a Derived Gene Fusion. Science 297:89-91.
 Leadbeater B and Kelly M. (2001). Evolution of
animals - choanoflagellates and sponges. NIWA Water & Atmosphere
9(2) Web article.
 Thomas NA, Bardy SL, Jarrell KF. (2001). The
archaeal flagellum: a different kind of prokaryotic motility structure.
FEMS Microbiology Reviews 25:147-174.
 Wolgemuth W, Hoiczyk E, Kaiser D, Oster G. (2002).
How Myxobacteria Glide. Current Biology 12:369–377.
 Bacterial Flagella:
A Paradigm for Design. ARN advertisement for the Flagella video.
of the Flagella video in the talk.origins news group.
 Behe MJ. (2001). Reply to my critics: A Response to
Reviews of Darwin's Black Box: The Biochemical Challenge to Evolution.
Biology and Philosophy 16(6):685-709. Also
 Musgrave I. (2000). Evolution
of Bacterial Flagella.
 Klose KE and Mekalanos JJ. (1998). Differential
regulation of multiple flagellins in Vibrio cholerae. Journal of
 Young GM, Schmiel DH, Miller VL. (1999). A new
pathway for the secretion of virulence factors by bacteria: The flagellar
export apparatus functions as a protein-secretion system. Proceedings of
the National Academy of Sciences of the USA 96:6456-6461.
 Thar R and Kühl M. (2002). Conspicuous Veils Formed
by Vibrioid Bacteria on Sulfidic Marine Sediment. Applied and
Environmental Microbiology 68(12):6310-20.
 Kirov SM, Tassell BC, Semmler AB, O'Donovan LA,
Rabaan AA, Shaw JG. (2002). Lateral Flagella and Swarming Motility in
Aeromonas Species. Journal of Bacteriology 184(2):547-555.
 Girón JA, Torres AG, Freer E, Kaper JB. (2002). The
flagella of enteropathogenic Escherichia coli mediate adherence to
epithelial cells. Molecular Microbiology 44(2):361-379.
 McGee DJ, Coker C, Testerman TL, Harro JM, Gibson
SV, Mobley HL. (2002). The Helicobacter pylori flbA flagellar
biosynthesis and regulatory gene is required for motility and virulence
and modulates urease of H. pylori and Proteus mirabilis.
Journal of Medical Microbiology 51(11):958-970.
 Foultier B, Troisfontaines P, Muller S, Opperdoes
FR, Cornelis GR. (2002). Characterization of the ysa pathogenicity locus
in the chromosome of Yersinia enterocolitica and phylogeny analysis
of type III secretion systems. Journal of Molecular Evolution 55(1):37-51.
 Young BM and Young GM. (2002). YplA Is Exported by
the Ysc, Ysa, and Flagellar Type III Secretion Systems of Yersinia
enterocolitica. Journal of Bacteriology, 184(5):1324-1334.
 Cornelis GR, Boland A, Boyd AP, Geuijen C, Iriarte
M, Neyt C, Sory MP, Stainier I. (1998). The virulence plasmid of Yersinia,
an antihost genome. Microbiology and Molecular Biology Reviews
 Stuber K, Frey J, Burnens AP, Kuhnert P. (2003).
Detection of type III secretion genes as a general indicator of bacterial
virulence. Molecular and Cellular Probes 17:25–32.
 Ussery D. (1999). Review of Darwin's Black Box.
Bios 70:40-45. There is an expanded version online.
Cavalier-Smith, T. (1997). The Blind Biochemist. Trends in Ecology and
Roger Dorit (1997). Molecular Evolution and
Scientific Inquiry, Misperceived. American Scientist 85(5):474-475. Also
of Darwin's Black Box at amazon.com.
 Links to The Institute for Creation Research,
Answers in Genesis and like minded groups are here.
The leaders of the intelligent design movement are all Senior Fellows
or higher at the Discovery Institute.
This essay first appeared at TalkDesign.Org