Building on quicksand?

PNAS Paper Admits Understanding the Origin of Cellular Features Is a "Glaring Gap" in Evolutionary Biology

Casey Luskin December 10, 2014 1:48 PM 

In 2001, biochemist Franklin Harold wrote in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations." Last month, a new paper in Proceedings of the National Academy of Sciences, "Evolutionary cell biology: Two origins, one objective," admitted much the same thing. The article states (emphasis added):

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. ... Because all evolutionary change ultimately requires modifications at the cellular level, questioning and understanding how cellular features arise and diversify should be a central research venue in evolutionary biology. However, if there is one glaring gap in this field, it is the absence of widespread cell-biological thinking. Despite the surge of interest at the molecular, genomic, and developmental levels, much of today's study of evolution is only moderately concerned with cellular features, perhaps due to lack of appreciation for their wide variation among taxa. However, a full mechanistic understanding of evolutionary processes will never be achieved without an elucidation of how cellular features become established and modified.

Co-authored by some leading evolutionary biologists who are also critics of the standard neo-Darwinian paradigm, the article suggests that evolutionary and cellular biologists need to focus on "bridging the gap" between their two fields. However, though the authors aren't necessarily neo-Darwinians, they retain the evolutionary materialist view that biological processes produce clumsy features, evidence of an absence of design. They want to understand how "historical contingency" and the "opportunistic process of 'descent with modification'" have produced living systems. Thus, they take an efficient molecular machine like the ATP synthase and consider the possibility that it's a poor solution to the problem of generating ATP:

One remarkable example of how history continues to influence today's cell biology is the near universal use of ATP synthase as a mechanism for energy generation. Embedded in the surface membranes of bacteria and organellar membranes of eukaryotes, this complex molecular machine uses the potential energy of a proton gradient to generate a rotational force that converts ADP to ATP, much like a turbine converts the potential energy of a water gradient into electricity. However, the proton gradient does not come for free: cells first use energy derived from metabolism to pump protons out of membrane-bound compartments, creating the gradient necessary for reentry through ATP synthase. Even assuming that ATP production is an essential requirement for the origin of life, it is by no means clear that the path chosen for ADP-to-ATP conversion is the only possibility.

However, they acknowledge that selection can't explain everything:

A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection. Leaving no room for doubt on the process, this narrow view leaves the impression that the only unknowns in evolutionary biology are the identities of the selective agents operating on specific traits. However, population-genetic models make clear that the power of natural selection to promote beneficial mutations and to remove deleterious mutations is strongly influenced by other factors. Most notable among these factors is random genetic drift, which imposes noise in the evolutionary process owing to the finite numbers of individuals and chromosome architecture.

Where selection fails, they propose forces like neutral drift. Yet as I explained here, under random genetic drift, features arise entirely due to random factors. At least natural selection offers some explanation as to how beneficial features are preserved. If selection has trouble building complex features, random drift would seem even more inadequate. Thus, incredibly, the paper argues that complex molecular machines evolved despite the fact that they may not have yielded a benefit:

Certainly, today's cells cannot survive without such molecular machines. However, the existence of complex cellular features need not imply that each of the myriad of changes that sculpted such structures over evolutionary time was adaptive at the time of establishment.

It seems doubtful that we can explain the origin of some of life's most complex, fundamental, and efficient machine-like features by appealing to random factors like random genetic drift, random recombination, and random mutation. This is hardly different from saying that molecular machines arose for no reason at all.

Be that as it may, their admission that explaining the origin of cellular features is a "glaring gap" shows that this remains a major problem for evolutionary thinking, whether under an adaptationist or a neutralist model. Though they don't put it quite as bluntly as Franklin Harold, this paper's message is no less potent: modern evolutionary biology lacks explanations for the origin of molecular machines.

More hand waving from materialists.

A Critic Asks: Doesn't Our C. elegans Video Commit the Post Hoc Ergo Propter Hoc Fallacy?

Paul Nelson April 20, 2015 11:39 AM | 

1. Does the video about C. elegans employ illicit "backwards" reasoning?

"How wise of the Creator," a lady is said to have remarked to a philosopher in an apocryphal exchange, "to have designed all the major rivers of Europe to run through its main cities." "And our noses were perfectly placed," a friend of hers added, "to support our spectacles."

Struck speechless by this double-barreled blast of blissful illogic, the philosopher could only manage a wan smile and shake his head.

A YouTube commenter, Vimal Ramachandran, argues that the video we just posted suffers from the samepost hoc ergo propter hoc ("after this, therefore because of this") fallacy. This merits a response. He wrote:

This is nonsense. Paul Nelson, you're making the mistake of looking at the end result -- a worm with muscle, nerves, germ cells, and intestine -- and concluding that this was the only possible outcome. Therefore, everything should have been programmed upfront to produce this particular creature with this particular characteristic. You then liken this to human architects who plan ahead to work towards a pre-decided end result.

But this is wrong and you won't understand evolution unless you free yourself from such teleological thinking. We know of even simpler animals that don't have such well-differentiated tissues or developmental patterns -- sponges, cnidarians, ctenophores, placozoans, all of which are evolutionarily even more ancient than C. elegans.

Thus, we can see that animals don't have to have nerves and muscles to survive, they started out as mere colonies of daughter cells, gradually acquiring specializations through evolutionary time. Different mutations produced different animal lineages which went different ways. One lineage led to the ancestor of C. elegans and its cousins including us. Random chance events and adaptation can explain this because the way C. elegans ended up was just one among countless possible outcomes, out of which only one outcome stuck. This outcome stayed on because it was good enough to produce a creature that can survive enough to reproduce in its given environment.

Likewise, another outcome stayed on for placozoans and yet another outcome stuck for sponges. It is wrong to look at the end result and see teleology. Rather, you must appreciate the role of how chance and contingency can produce diverse patterns from a simple beginning. I'm worried about young students who will be misled by such wrong propaganda.

To which I can only add: of course.

Of course animals don't need to have the anatomical features or the developmental pathways ofC. elegans. Sponges don't, nor do placozoans, nor do cnidarians, or ctenophores -- and so on.

But that's not the problem. C. elegans does need its specific features. And that IS the problem to be solved.

Let's assume that all animal species, including C. elegans, share a common ancestor, which is what evolutionary theory claims. This geometry entails -- necessarily requires -- a sequence of intermediate forms leading to C. elegans from its unicellular eukaryotic ancestors. Now, whatever those intermediates happened to be, the lineage they constitute must arrive at C. elegans, with all of its developmental details and features, somehow. The target for explanation is thus provided by nature herself.

Saying this doesn't invoke teleology or post hoc reasoning in the least. Rather it's a straightforward deduction from the existence of C. elegans, given the theory of common descent. If C. elegansindeed evolved by an undirected historical process, the lineage leading to the species through space and time, from other different species, must have existed. And the target of interest, namely, C. elegans itself, is here today and requires explaining, whether we assume teleology or not.

So what evolutionary lineage constructed C. elegans?

2. Focusing on what's relevant

Suppose your doorbell rings, and you open the front door to find me standing there. You live on the 37th floor of an apartment building, at the end of a long brick hallway with no other doors or windows. The building has one elevator reaching the 37th floor, a single stairwell, one public entrance with a security desk staffed at all hours, and is located in Manhattan.

These facts constrain the possible explanations that we can reasonably consider about how I came to be standing at your front door. To say, "But Paul could have gone to hundreds of other apartments in that building, or to another building altogether, or to Boston, or London," is true, but strictly irrelevant. Those possibilities concern other outcomes -- but not the explanatory target of interest. If we wish to explain why I am standing in your hallway, that's the universe of relevant information. Likewise, if we wish to explain the origin of C. elegans, focusing on unrelated species only defers the task, or misdirects our attention to irrelevancies.

Vimal Ramachandran writes:

...animals don't have to have nerves and muscles to survive, they started out as mere colonies of daughter cells, gradually acquiring specializations through evolutionary time. Different mutations produced different animal lineages which went different ways. One lineage led to the ancestor of C. elegans and its cousins including us.

Okay, let's go with this hypothesis. Here are some questions that must be answered:

• What colonial (or other) species were the ancestors of C. elegans?
• How did cells in those species gradually acquire the specializations seen in C. elegans?
• What mutations in those species produced the anatomical features or developmental pathways of C. elegans?

Nobody knows, including Vimal Ramachandran -- which is why his explanation is so hopelessly vague and hand waving. Once one begins actually to grapple with the precise details of C. elegansdevelopment, for instance, "gradually acquiring specializations" immediately turns into a just-so story of zero value.

3. This problem won't go away, and calling it teleology won't make it go away

The point of the videos is to highlight what needs to be explained when we come to a well-understood system such as C. elegans. In particular, the origin of the developmental stages between fertilized egg and reproductively capable adult are hard (or impossible) to explain via natural selection. This problem was the topic of my poster at the 2014 annual meeting of the Society for Developmental Biology.

Vimal Ramachandran's objections would be weightier if they had any genuine substance. I'll stic k with the evidence.