VII. Why
Do Things Have to Be So Complicated?
Interviewer: What do you mean by functional
complexity?
Schützenberger: It is impossible to grasp the
phenomenon of life without that concept, the two words each expressing a
crucial idea. The laboratory biologists’ normal and unforced vernacular is
almost always couched in functional terms: the function of an eye, the function
of an enzyme, or a ribosome, or the fruit fly’s antennae. Functional language
matches up perfectly with biological reality. Physiologists see this better
than anyone else. Within their world, everything is a matter of function, the
various systems that they study—circulatory, digestive, excretory, and the
like—all characterized in simple [and] functional
terms. At the level of molecular biology, functionality may seem to pose
certain conceptual problems, perhaps because the very notion of an organ has disappeared
when biological relationships are specified in biochemical terms. But
appearances are misleading. Certain functions remain even in the absence of an
organ or organ systems. Complexity is also a crucial concept. Even among
unicellular organisms, the mechanisms involved in the separation and fusion of
chromosomes during mitosis and meiosis are processes of unbelievable complexity
and subtlety. Organisms present themselves to us as a complex ensemble of
functional interrelationships.
The simplicity and tidiness of the mechanistic worldview has
proved ideal for school textbooks and an increasing number of publications
written for laypeople, a genre we know as pop-science.
No author consciously intends to limit their readers’ awareness of our world’s
complexities (which, indeed, usually require at least some explanatory simplification for the sake of clarity). However,
widely read books continually portray the workings of life in an unnecessarily
simplistic fashion. Oversimplification doesn’t profit our technically fluent
society—one that thrives on
complexity—but may be an unavoidable consequence of the need to reach readers
with broad ranges of knowledge.
In truth, everything
having to do with living matter is staggeringly complicated—with no exception.
Educators necessarily simplify descriptions of life-processes to bring such
matters within intellectual reach; those who actively promote a conception of
nature operating by “simple” rules are furthering a reductionist, mechanistic
viewpoint.
Take any generalized account of, say, cell division: readers
will be warned of this being a highly involved affair. Following that
disclaimer, multiple layers of mentally numbing complexity aren’t merely
deemphasized—usually they will not even be alluded to…or even touched upon as a
sort of reminder that can prove helpful in acquiring perspective on complicated
subjects. Incurious readers seldom think to ask tough questions, having been
schooled to assume that the entire train of events takes place automatically
and isn’t especially noteworthy to begin with. After all, It’s just chemistry!
Moreover, as fresh data and new findings compel the revision of
biological models to reflect added details and nuances, there is typically a
considerable time lag in imparting the latest information. (In fact, presenting
up-to-date facts and ideas my readers may not have heard about is a major
reason for taking on this work.) Another aspect of this struggle with getting
current knowledge to the public can be traced to school textbooks; many are
repeatedly revised and distributed in the form of new editions without
antiquated information being checked for veracity and retired as needed; a good
deal of superseded or inaccurate material is disseminated in this fashion.[2]
Finally, the broad range of informational veracity found on the internet has
created further impediments to attaining quality knowledge.
Long after it should have become universally recognized that
cells are far more complicated than was previously imagined, they continue to
depicted in a manner that makes light of
their extraordinary intricacy. Researchers continue to unravel our thorniest problems and many biologists
believe that, sooner or later, various lingering unknowns will be clarified. Meanwhile,
thanks to biological complexity being undervalued in textbooks and works of
pop-science (plus a tendency to flagrantly dumb-down media and internet
renderings), our “scientifically engaged” public has acquiesced to a flawed and
deficient view of how the living world functions.
The discovery of self-assembly explains many
events in cells that once seemed utterly mysterious. It is akin to learning
that the steel skeleton of a building will assemble spontaneously once a load
of girders is dumped at a construction site. The genes cause a load of protein
molecules to be synthesized in the cell, but the proteins, needing no further
control, spontaneously assemble themselves into larger structures. The plan of
the final result is implicit in the structure of the components.
To back up this assertion, he then cited two
classic examples of structural self-assembly: the case of microtubules (which
spontaneously form when molecules of tubulin—a protein synthesized in all
cells—join together in a uniform spiral pattern) and the self-ordering of
phospholipids into the bilayer membranes common to all eukaryotic cells.
Rensberger promotes a sense that such auto-assemblage is marvelous, yes, but simply the result of an opportune coincidence
of chemical properties.
Rensberger’s descriptions are a bit
misleading, though, given that the two key processes are far from entirely
automatic (plus, the components have to first be fabricated within the cell).
In the case of microtubules, a number of specialized protein machines assist
with the construction of new (and degradation of old) tubules along with their
attachment to organelles or the cell wall. As for lipid bilayers: thanks to the
powerful chemical attraction of lipids in an aqueous solution, they do readily
assemble into sheets and vesicles…but functional cellular membranes are
actually constructed piecemeal within the cell by the endoplasmic reticulum,
then further processed in the golgi, and finally transported in vesicular form
to fuse with the targeted membrane.
In the second excerpt, he again de-emphasizes complexity in
favor of furthering an impression of straightforwardness and simplicity:
Amazingly enough, some of the regulatory DNA
sequences are not situated near the gene they control. They may be hundreds or
tens of thousands of bases away. And yet, if the right regulatory proteins
don’t bind to them, the gene won’t be expressed. How can this be? How can the
gene or the RNA polymerase “know” whether certain proteins have grabbed onto
the DNA strand…? Simple. DNA is flexible. It simply forms a loop in itself,
bringing the distant regulatory protein into contact with other proteins on the
promoter. In the case of the beta hemoglobin gene, there are several
regulators…that speed up the gene-activation rate to varying degrees and some
that slow it down to varying degrees. Somehow they work it out among themselves
how often the gene should be allowed to express itself.
These
two examples are typical—not nearly as striking as other cases I’ve
encountered—of the cavalier language and rhetoric used to explain such
phenomena. Many modern books about these types of subjects are peppered with
similar instances; when some involved process requiring multiple steps and
coordinated assistance is described, the whole affair is frequently put across
in a fashion that deftly underplays its elaborate nature. (A later section will
examine this phenomenon more closely.)
Unquestionably,
individual molecular interactions are events involving straight-forward
chemical and electrical attractions (or repulsions). The occasional use of
superlatives like “amazing” and “wondrous” in books like Rensberger’s Life Itself merely allude to the uncanny
ways in which inanimate molecules behave. The reader is routinely assured that
such things happen automatically and according to just such types of rationally
ordered but non-intentional activity (often with emphasis on there being no
mysterious agencies involved—so strange can these happenings seem to
non-scientists).
No
doubt many, if not most, of the sort of complicated issues I’ve broached have
been at least partially explained. However, answers to the kind of questions
I’ve posed don’t seem to be included in pop science books. The information I
seek is to be found in the plethora of technical literature published in
scientific journals.[3]
One
thing I’ve noticed, reading technical papers—a noticeable pattern: various
molecular participants arrive on the scene of some reaction to play a part in
some key process with no word of how they were manufactured, where they came
from, or what regulatory agency was involved in their appearance. Such
tangential information may have been deemed non-essential or beyond the subject
matter’s scope…but its absence often strikes me as intentional (possibly
unknown?). Things simply “show up.”
And
show up they do. In their frenetic comings and goings, molecules display a sort
of purposefulness that only higher-level organisms are thought to enjoy. Are their coordinated actions, taken
together, purely mechanical? Microbiologist James Shapiro writes about “the
growing realization that cells have molecular computing networks which process
information about internal operations and about the external environment to
make decisions controlling growth, movement, and differentiation”:
Bacterial and yeast cells have molecules
that monitor the status of the genome and activate cellular responses when
damaged DNA accumulates. The surveillance molecules do this by modifying
transcription factors so that appropriate repair functions are synthesized.
These inducible DNA damage response systems…include so-called “checkpoint”
functions that act to arrest cell division until the repair process has been
completed…. One can characterize this surveillance/inducible repair/checkpoint
system as a molecular computation network demonstrating biologically useful properties
of self-awareness and decision-making.
This
is not a conventional portrayal of mindless molecules at work. Recall that, in
the second excerpt from Life Itself,
Rensberger wrote of regulatory enzymes: “Somehow they work it out among
themselves.” Obviously, the author didn’t intend to allege truly purposive
action being displayed in using this offhand way of explaining the solution to
an arcane problem, but simply wanted to carry on with his narrative. In the
course of my research, though, never have I seen so much as a hint of there
being anything out of the ordinary about the way protein machines bustle about
in resolute teams, with individual
members making crucial decisions.
Returning
to my original statement regarding the nature of life: it has its own intelligence and a quality of
self-directedness that is displayed by all organisms—even manifesting at the
molecular level. It would be a mistake to equate this form of willful
discernment with its human analogue. Nonetheless, these traits are called to
mind as it becomes ever more obvious that living things function according to
singular kinds of molecular organization—with involvements that go way beyond
the ordinary chaotic collisions that make things proceed in cell-world. And
behind all such activity there is often an element suggestive of intent.
In
fact, enzymes display intelligence-mimicking behavior in the form of a
functional property called allostery,
made possible by an enzyme’s capacity to change shape such that an active site
can no longer bind with its substrate.
Say
a particular enzyme’s job is to catalyze a reaction that produces a chemical
whose concentration causes problems, maybe even a fatal toxicity, when
exceeding certain limits. How does it “know” when to stop? Solution: the
catalyzed reaction’s product (or, if the reaction results in more than one
product, one of its elements) also serves as a control molecule. When this product’s concentration reaches a
certain level, it starts binding to a second active site on the enzyme,
changing the enzyme’s shape so that the substrate is no longer able to dock…and
production of the chemical in question ceases. This is what’s known as a negative feedback loop, a vital feature
exhibited throughout nature from the nano-scale to the planetary (where, for
instance, forms of self-correcting regulation are seen at work in the carbon
and hydrological cycles).
Allostery
forms the basis of regulation in cells. Physicist-turned-microbiologist Peter
Hoffman adds further perspective on the intricacy of these regulatory systems:
There are more complicated schemes that
involve vast networks of interacting enzymes. The product of one enzyme may act
as the control molecule for another enzyme, either enhancing or inhibiting its
activity. The product of this second enzyme may again control the first enzyme,
forming a two-enzyme feedback loop…or the product may influence a third enzyme,
which influences a fourth, and so on. Complicated schemes of feedback loops and
mutual enhancement or inhibition provide the computing power that makes living
cells seem intelligent.
This
dual-functionality of proteins—their ability to both carry out reactions and
adjust results to some necessary end—is a crucial feature in the regulation of
cellular metabolism. Allosteric enzyme activity is essential to prevent the
chemical chaos that would result if not delicately tuned to a cell’s strict
requirements. Jacques Monod, who discovered the phenomenon in Paris in the
early 1960s while working on bacterial cell metabolism, felt the significance
of allostery to be so indispensable that called it “the second secret of life.”
(The “first” being the genetic code itself.) Horace Judson, in The Eighth Day of Creation:
Allosteric proteins were relays, mediating
interactions between compounds which themselves had no chemical affinity, and
by that regulating the flux of energy and materials through the major system,
while themselves requiring little energy, The gratuity [“the freedom from any chemical or structural necessity in
the relation between the substrate of an enzyme and the other small molecules
that prompted or inhibited its activity”] of allosteric reactions all but
transcended chemistry, to give molecular evolution a practically limitless
field for biological elaboration.
These
are all attributes whose subtlety deserves more emphasis whenever cellular
functions are under discussion. Instead, we find a marked tendency to
de-emphasize the sophistication of features such as auto-regulation. By the
same token, it’s not just the subtlety and phenomenally clever quality of all
these things, but the way they are all entangled and their activities so
precisely coordinated. This higher order of interaction is what has such
weighty implications: this is where
the impression of intelligence and intentionality is grounded.
For
instance, during cellular division: How do all the players involved initially
gather and position themselves? How do they know exactly when to perform
their assignments, avoid interfering
with other teammates, and recognize when to cease and desist? How do they all
get to the game on time? What “master gene” calls them to their tasks? What
controls those master genes?
I
can hear the skeptic’s answer: Yes, yes,
yes…we know how each of these things take place: it’s all by gene-controlled
chemical signals…markers, couriers, vesicular transport. Regulatory genes.
Allosteric proteins. The subtlest details are being worked out at this very
moment; these automatic processes are all well-understood, at least in general
outline. It’s all chemistry!
About
those “upper-echelon proteins”—whether self-regulating or controlled by
genes…the ones that initiate and direct the actions of whole assemblages of
nano-scale machines: how do they
fulfill their roles? What orders them up and accounts for all the functions
carried out in their vital, higher-level tasks? How are the actions of
allosteric enzymes coordinated with those of genes, when neither has
controlling influence over the other? And one last element that exposes yet
another aspect of these profound, multifaceted interactions: time. During the
many stages of mitosis, including DNA replication, all the cell’s genes are
dormant. (In the case of humans, this means for some hours.) Hence, all
instructions relevant to division have to be issued beforehand; all the suites
of enzymes and protein machinery involved have to be synthesized, tagged for
recognition, and somehow “programmed” in advance. Many individuals will need to
be repaired or replaced while they wait. Once provided with their orders,
though, they join the throngs careening about the cell, killing time until they
hear a bell ring.
Andreas
Wagner, specialist in the new field of
computational biology, provides an answer (of sorts) to all these quandries
and seeming bottlenecks. (This elucidation is likely about as straightforward
as can be achieved using plain language.) He writes:
The answer lies in regulation…. And what
regulates the regulators? Simple: more regulators…. And what about these
regulators, how are they regulated? Through other regulators. All these
regulators often form daisy chains, regulation cascades….[This] would seem
enough complexity…but alas, regulation can get much more complicated: Regulators form not just linear chains but
complex…circuits where regulators
regulate each other…. Each [activates or represses] a gene [and] can twiddle
the knobs of other genes—up to hundreds—outside the circuit…. Inside a cell
these influences create a symphony of mutual activation and repression, where
each instrument in the orchestra of genes responds to the melodic cues of
others with its own notes, until the circuit reaches an equilibrium—like a
polyphonic closing chord—where the expression of circuit genes no longer changes and their
mutual influences have reached a balance.[4]
Wagner’s
portrayal of symphonic regulation provides an ideal context for the asking of
three Big Questions that approach the heart of what I’ve termed Natural Design: At what point do all these circles close?
What is the nature of these highest levels of organization and control? Can
something be identified that, ultimately, is “in charge”?
Whatever
it is, whatever might be considered the “conductor,” appears to operate by way
of a multilayered complexity that is beyond description or even our limited
imagination. This…thing…is rooted in the underlying character of life. Immanuel Kant (whose insights are
still pertinent today) thought the whole subject inaccessible to causal
explanation. As he urged, we may be better served by simply taking life’s nature as a given and let biology
proceed from that starting point (thus saving both philosophers and scientists valuable
time that they could put to better use). There is, after all, some precedence
for this stance, it being essentially the way we treat matter, time, and the
elemental forces—core principles not subject to further elucidation.
Regardless:
hopefully all my readers have come around to the notion that nature is
inherently complicated and, as such, biological systems require consideration
and study with an explicit recognition of this complexity—even though such
practice will unavoidably hamper straightforward communication. This exacting
way of viewing natural processes will always present conceptual challenges
given that the intellectual capacity to sustain awareness of many things
interacting simultaneously is a gift few are endowed with. However, such
awareness—even an approximation—is essential in the effort to understand life.
Few
would disagree with these propositions. Still, I continually see an acute lack
of appreciation for the subtext beneath nature’s profound intricacy…a
resistance to the idea that this ineffable quality has pivotal meaning on its
own. Biological complexity is rooted in one of life’s most distinct attributes—the
capacity of its productions to be both self-governed and harmoniously
organized. This shadowy, indefinable quality can’t specifically explain the things examined in this
section but provides structural support for reassessing the so-called emergent properties—patterns,
behaviors, or traits that can’t be deduced from either lower or higher levels
of association. (The deliberate, organismic behavior of DNA helper molecules being a fine example.)
At
present, however, many people—including leading experts in their fields—often
create an impression of not being fully awake to this crucial truth: in
biological systems, at all scales and each level of organization, different
types of the attribute Marcel-Paul
Schützenberger termed functional
complexity are in operation. At each organizational stratum, new structures
or regularities appear: the property of emergence.
And each stratum calls for its own manner of describing relationships between
parts or processes that often aren’t even present at levels above or
below.
Once
again: life is much more than the
elaborate interaction of molecules.
©2016
by Tim Forsell draft 30 Apr 2016
[1] Dembski’s book is a collection of essays. The majority
of contributors, like Dembski himself, are staunch creationists with obvious
agendas. Others, scientists all, are not
anti-evolution but at odds with various aspects of Darwinism (some of which
have been addressed and even resolved since the essays were written).
Schützenberger (1920–1996) was in the latter group; he was a member of the
French Academy of Sciences, a medical doctor, mathematician, and according to a
memoriam, “was passionately interested in the many flaws in the Darwinian
theory as it is commonly presented…. [He] became one of the first distinguished
scientists in the world to point out that a theory of evolution that depends on
uniformly randomly occurring mutations cannot be the truth because the number
of mutations needed to create the speciation that we observe, and the time that
would be needed for those mutations to have happened by chance, exceed by
thousands of orders of magnitude the time that has been available.” This
interview was originally printed in La
Recherche [The Remembrance], a French science monthly, shortly before his death.
[2] Paleontologist Simon Conway Morris referred to such
information being “still routinely cited…in that zoo of good intentions, the
undergraduate textbook.” A classic example
is the formerly ubiquitous embryo drawings by Ernst Haeckel illustrating his
long-discredited “biogenic law” with its notorious tongue-twisting axiom,
“ontogeny recapitulates phylogeny,” found in generation after generation of biology
texts. Only 30 years after Haeckel produced the compelling drawings (around the
turn of the 20th century) his biogenic law had been refuted, yet
they continued to appear in textbooks for decades.
[3] Twenty thousand
scientific papers were being published daily,
according to a figure quoted in Calder. Also: as of 2010, there were about
24,000 different scientific journals in all fields. This figure, which includes all aspects of natural and social
sciences, plus arts and humanities, is quoted in Larsen and von Ins.
[4] While remaining true in spirit, this excerpt is a
significant reduction of Wagner’s much lengthier account.
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