Reading through a recent article by KeithS over at The Skeptical Zone, I was reminded of the following lyrics from the musical Annie Get Your Gun:
Anything you can do,
I can do better.
I can do anything
Better than you.
No, you can’t.
Yes, I can. No, you can’t.
Yes, I can. No, you can’t.
Yes, I can,
Yes, I can!
The article, which is entitled, Things That IDers Don’t Understand, Part 1 — Intelligent Design is not compatible with the evidence for common descent, argues that evolution guided by an Intelligent Designer fares much worse – in fact, trillions of times worse – than unguided Darwinian evolution as an explanation of how living things arose in all their diversity, because whereas Darwinian evolution is the only way in which unguided natural processes could have generated the life-forms we see on Earth today, the probability of an Intelligent Designer choosing to make living things in a way that mimics unguided Darwinian evolution is very, very low: there were so many other ways in which the Designer might choose to produce life on Earth rather than by mimicking such a process.
KeithS’s article discusses a very striking feature exhibited by living things: the fact that they fall into “groups within groups”, or what biologists refer to as a nested hierarchy. EvoWiki provides a useful definition of this term:
“Nested hierarchy” refers to the way taxonomic groups fit neatly and completely inside other taxonomic groups. For instance, all bats (order Chiroptera) are mammals. All mammals are vertebrates. Likewise, all whales (order Cetacea) are also mammals, and thus also vertebrates.
While it might seem that this arrangement is obvious and unavoidable, it is not. Taxonomic groups are defined by traits and it should be possible to mix traits from multiple defined groups. An example from classical mythology is the Pegasus, a creature with features defined as both mammal (produces milk like a horse) and bird (has feathers). Mammals and birds are both orders, so, if Pegasus existed, it would be a violation of the nested hierarchy, a creature that belonged to two separate groups. Likewise for satyrs (human torso, goats legs), jackalopes (rabbit body with an antelope head) and crocoducks (crocodile head, body of a duck)…
Life, however, shows a clear nested hierarchy, at least with regards to multicellular organisms. An animal that produces milk (Mammals), will also have hair, have four limbs, be endothermic (warmblooded) plus possess many other characteristics. Why should this be? Why do no other animals or plants produce milk? Why do no mammals have four limbs plus a pair of wings, like the Pegasus or angels?
Hierarchies are a very common feature of the world in which we live. However, not all hierarchies are nested hierarchies. Nested hierarchies involve levels which consist of, and contain, lower levels. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. Non-nested hierarchies, on the other hand, are more general, in that they relax the requirement that higher levels should contain the levels below them. For instance, the general at the top of a military command does not consist of his soldiers: they are distinct from him, and he doesn’t “contain” them. Thus the military command (unlike the army) is a non-nested hierarchy, with regard to the soldiers in the army. In general, all pecking orders are non-nested hierarchies. And in the natural world, food chains are excellent examples of non-nested hierarchies.
Dr. Douglas Theobald explains why the nested hierarchy we find in living things is such a powerful piece of evidence for Darwinian evolution in his article, 29+ Evidences for Macroevolution: The Scientific Case for Common Descent (Prediction 1.2: A nested hierarchy of species):
As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as “groups within groups”, otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics…
…[I]f common descent is true, then in some time frame we will always be able to observe a nested hierarchy for any given character. Furthermore, we know empirically that different characters evolve at different rates (e.g. some genes have higher background mutation rates than others). Thus, if common descent is true, we should observe nested hierarchies over a broad range of time at various biological levels. Therefore, since common descent is a genealogical process, common descent should produce organisms that can be organized into objective nested hierarchies.
For anyone who may be wondering what a Markov process is, Wikipedia provides an easily accessible definition:
A Markov chain (discrete-time Markov chain or DTMC) named after Andrey Markov, is a mathematical system that undergoes transitions from one state to another, between a finite or countable number of possible states. It is a random process usually characterized as memoryless: the next state depends only on the current state and not on the sequence of events that preceded it. This specific kind of “memorylessness” is called the Markov property.
I’d now like to discuss the recent article by KeithS, over at The Skeptical Zone. His key point is a very simple one. What Darwinian evolution explains spectacularly well about life is the striking fact that organisms can be grouped into objective nested hierarchies. As we saw above, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains, which automatically generate nested hierarchies in replicating systems that branch. The process of Intelligent Design, on the other hand, need not generate organisms that can be grouped into objective nested hierarchies: all we can say is that it might.
A puzzle about an apartment dweller
Marina City in Chicago, Illinois, United States, which was built in 1959, was a landmark in apartment construction. Image courtesy of Wikipedia.
In order to properly appreciate the point that KeithS makes in his article, let’s consider the following puzzle (which some readers will have encountered before) about an apartment dweller with a rather strange habit:
A man lives on the 26th floor of an apartment building. He takes the elevator every day, when he goes to work. When he comes back from work, he doesn’t take the elevator up to the 26th floor, where he lives. Instead, he takes the elevator up to the 12th floor. Why does he do this?
When I put this puzzle to people who haven’t heard it before, most of them come up with an ad hoc rationalization: “Maybe he needs the exercise,” “Maybe the elevator is very crowded in the evening, so he gets out half-way up because he needs to get some fresh air,” or “Maybe he has a girlfriend who lives on the 12th floor.” These are perfectly fine explanations of why the man might get off at the 12th floor, but they all share a common failing: they fail to explain why he must get off at that floor. There’s only explanation that can account for this singular fact, and as soon as we hear it, we instantly recognize that it must be the right explanation: the man is a dwarf, and he can’t reach the button for the 26th floor.
What KeithS is arguing, then, is that Darwinian evolution is the true explanation for the striking fact that living things fall into “groups within groups” (or what we call a nested hierarchy) because it’s the only account that tells us why they must exhibit this property, whereas Intelligent Design explanations of this fact are merely ad hoc rationalizations which at best, can only tell us why living things may fall into a nested hierarchy. Thus Darwinian evolution wins “hands down”, as an explanation of the nested hierarchy into which living things can be classified.
KeithS: Why Darwinian evolution is a much better explanation of the nested hierarchy into which living things can be classified than intelligently guided evolution
It might seem as if the foregoing argument would only work against Intelligent Design proponents who reject common descent and who hold that each kind of organism was created separately. But KeithS contends that even Intelligent Design advocates like myself, who accept the evidence for common descent, are unable to provide a good explanation for the nested hierarchy we find in living things. The problem is that whereas Darwinian evolution automatically generates this nested hierarchy, guided evolution does not, which means that people who support guided evolution have to fall back on the lame, ad hoc explanation that “the Designer just wanted it that way”:
In other words, our ‘common descent IDers’ face a dilemma like the one faced by the creationists. They can force guided evolution to match the evidence, but only by making a completely arbitrary assumption about the behavior of the Designer. They must stipulate, for no particular reason, that the Designer restricts himself to a tiny subset of the available options, and that this subset just happens to be the subset that creates a recoverable, objective, nested hierarchy of the kind that is predicted by unguided evolution. Unguided evolution doesn’t require any such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation. And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.
In a nutshell: KeithS contends that a Design-based explanation of the nested hierarchy into which living things can be classified is inferior to a naturalistic one, because it doesn’t specifically generate a nested hierarchy, whereas an unguided, naturalistic evolutionary process does. As Dr. Douglas Theobald puts it: “The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes” (italics mine).
And because the nested hierarchy into which living things can be classified isn’t just an “incidental” feature of living things, but an all-pervasive, defining feature that applies to all kinds of organisms, we can confidently say that Darwinism is a much better explanation of life in general than Intelligent Design.
Case closed, right? Not so fast.
Why cars don’t work as a counter to KeithS’s argument
A photograph of the original Benz Patent-Motorwagen, first built in 1885 and awarded the patent for the concept. Image courtesy of Wikipedia.
Before I put forward an Intelligent Design explanation of the nested hierarchy that all species of living things belong to, I’d like to discuss a bad explanation for the nested hierarchy which in my opinion simply doesn’t work.
Dr. Theobald, author of 29+ Evidences for Macroevolution: The Scientific Case for Common Descent, is well aware of the common creationist counter-argument that some designed artifacts, such as cars, also exhibit a nested hierarchy like the one we find in Nature. Actually, he says, most artifacts don’t exhibit an objective hierarchy, in the way that living things do:
Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically — perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective.
… Which types of car characters are more important depends upon the
personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.
Dr. Theobald goes on to say that inanimate objects typically don’t fall into nested hierarchies, whereas living organisms do:
Interestingly, Linnaeus, who originally discovered the objective hierarchical classification of living organisms, also tried to classify rocks and minerals hierarchically. However, his classification for non-living objects eventually failed, as it was found to be very subjective. Hierarchical classifications for inanimate objects don’t work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors.
The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of “cladistic hierarchical structure” (also known as the “phylogenetic signal”) in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).
A nested hierarchy is a necessary property of individual organisms and of ecosystems
Dr. Theobald’s reply is a telling one. But before we continue, let’s ask ourselves this question: why don’t cars and other inanimate objects exhibit an objective nested hierarchy? Dr. Theobald thinks it’s because they’re not related by common descent, as living things are: the first car didn’t “beget” its successors, such as the Model T or the Ford Mustang. I disagree: I think it’s because they’re not alive. What I’m going to propose is that the nested hierarchical taxonomy into which the various kinds of organisms can be classified, and the nested hierarchical structure of an ecosystem, which is composed of populations of organisms, each of which is composed of organs, tissues and cells, are really two sides of one and the same coin. I would also contend that nested hierarchy of structure is an essential property of organisms, but not of artifacts such as cars.
In an article entitled, “Hierarchy: Perspectives for ecological complexity” (The Philosophy of Ecology: From Science to Synthesis edited by David R. Keller and Frank Benjamin Golley, University of Georgia Press, 2000), authors T. F. H. Allen and Thomas B. Starr describe two nested hierarchies that pervade the entire field of biology: the taxonomic hierarchy, which reflects the way in which each and every kind of living thing can be scientifically classified (a species belongs to a genus, which belongs to a family, which belongs to an order, which belongs to a class, which belongs to a phylum, which belongs to a kingdom, which belongs to a domain), and the structural hierarchy that we find not only within the body of each individual organism (which is made of up of organ systems, which are made up of organs, which are made up of tissues, which are made up of cells), but also within the larger community to which it belongs: an individual is a member of a population of organisms, which belongs to an ecosystem:
The notion of hierarchical arrangement is central to biology and even has an Aristotelian origin. The two standard ways of organizing biological systems, that is, into taxonomic units and structural relationships, both represent nested hierarchies. A nested hierarchy is one where the holon at the apex of the hierarchy contains and is composed of all lower holons. [A holon is something that is both a whole and a part. You are a whole, as an individual. You are also a part of society: no man is an island. – VJT] The apical holon consists of the sum of the substance and the interactions of all its daughter holons, and is, in that sense, derivable from them. Individuals are nested within populations, organs within organisms, tissues within organs, and tissues are composed of cells. In taxonomy a family consists of its constituent genera and their component species. These two hierarchical arrangements are ubiquitous in modern biology to such an extent that these arrangements are commonly used to order the material in introductory textbooks. (p. 228)
The authors go on to point out that there are also many non-nested ecological structures. But the point I’d like to make here is that the taxonomic hierarchy described by Dr. Theobald 29+ Evidences for Macroevolution: The Scientific Case for Common Descent and discussed by KeithS in his recent post isn’t the only nested hierarchy in the field of biology: it exists alongside a structural hierarchy that we also find in Nature. Dr. Lukas Buehler, in his life science forum “What is Life?”, provides an excellent summary of this nested structural hierarchy on a Web page entitled, Life can be studied as a hierarchical structure.
Now, it is easy for most laypeople to recognize that the body of a multicellular organism is a nested hierarchy with multiple levels, being made up of organ systems, which are made up of organs, which are made up of tissues, which are made up of cells. What is not so commonly appreciated, however, is the fact that the ecosystems to which these organisms belong are also nested hierarchies. This can be readily verified if one examines the various definitions of the term Ecosystem that can be found in the Environmental Benefits Analysis (EBA) program glossary published by the U.S. Army Corps of Engineers. Among the definitions listed are the following:
Definition: a spatially and functionally nested hierarchy of air, land, and water units that include all the biotic and abiotic components within its boundaries.
Source: EBA Workgroup Manuscript : Smith et al and (Forman and Godron 1986, SERI 2004). The Role of Reference in Ecosystem Restoration.
Definition: a biotic community, together with its physical environment, considered as an integrated unit. Implied within this definition is the concept of a structural and functional whole, unified through life processes. Ecosystems are hierarchical, and can be viewed as nested sets of open systems in which physical, chemical and biological processes form interactive subsystems. Some ecosystems are microscopic, and the largest comprises the biosphere. Ecosystem restoration can be directed at different-sized ecosystems within the nested set, and many encompass multi-states, more localized watersheds or a smaller complex of aquatic habitat.
Source: HEAT Manual – Burks-Copes et al. 2008
Definition: A biotic community, together with its physical environment, considered as an integrated unit. Implied within this definition is the concept of a structural and functional whole, unified through life processes. Ecosystems are hierarchical, and can be viewed as nested sets of open systems in which physical, chemical and biological processes form interactive subsystems. Some ecosystems are microscopic, and the largest comprises the biosphere. Ecosystem restoration can be directed at different-sized ecosystems within the nested set, and many encompass multi-states, more localized watersheds or a smaller complex of aquatic habitat.
Source: MRGBER Feasibility Study Habitat Assessment : Analyses, Results and Documentation (Burks-Copes et al.)
Definition: An ecosystem is the dynamic and interrelating complex of plant and animal communities and their associated nonliving environment, considered as an integrated unit. Implied within this definition is the concept of structure and function unified through life processes. An ecosystem may be characterized as a viable unit of community and interactive habitat. Ecosystem restoration can be directed at different sized ecosystems within the nested set, and may encompass multiple states, more localized watersheds, or a smaller complex of aquatic habitats.
Source: Planning and Guidance Notebook, Engineer Regulation 1105-2-100, 22 April 2000
In short: living things embody, in their very anatomy, a nested hierarchy of ends. What’s more, a nested hierarchy is also an inherent feature of the ecosystems to which individual organisms belong. But why would this structural hierarchy of life go hand in hand with a corresponding taxonomic hierarchy?
In order to answer this question, we first need to understand a fundamental property of living organisms: their dedicated functionality. The entire functional repertoire of each part of a living thing is “dedicated” to supporting the functionality of the organism it belongs to. (Note: By “the entire repertoire” of a part, I mean everything that it currently does. The parts of a living thing may have other potential uses: genes and even organelles can be exchanged between organisms, as shown by the phenomena of lateral gene transfer and endosymbiosis, respectively.)
Dr James Tour, the T. T. and W. F. Chao professor of chemistry and computer science at Rice University, explains the concept of embedded functionality using the illustration of a tree:
Dr. Tour explains: “[Let’s say that] you see a tree [and] you want to make a table, [so] you chop down the tree [and] you make a table – that’s [building] top down. But, the tree and I and everything else in nature are built from the bottom up. Molecules have certain embedded interactions between them and embedded functionality. Those come together to form higher-order structures called cells and those form higher-order structures and here we are.” You might also envision this as building from the inside out, or by forming the required traits in the smallest conceivable building blocks first.
(Interview with D. Geer: “Organic Computing: Life that Computes”, in TechWorthy.com magazine, Bedford Communications, 2002.)
I might mention in passing that this method of building living things is precisely the opposite of the way in which many critics of Intelligent Design (both religious and non-religious) imagine that God would produce living things. For instance, in a comment on a post entitled, Nature versus Art (April 30, 2011), Professor Feser asserted that God could, if He wished, make a man from the dust of the ground, simply by saying, “Dust, become a man.” When I asked him about the sequence of steps involved in such a transformation, he wrote back:
Forming a man from the dust of the ground involves causing the prime matter which had the substantial form of dust to take on instead the substantial form of a man. I’m not sure what “sequence of steps” you have in mind. There’s no sequence involved (nor any super-engineering – God is above such trivia). It’s just God “saying,” as it were: “Dust, become a man.” And boom, you’ve got your man.
… We have to work through other pre-existing material substances and thus have to do engineering and the like in order to make things. God, who is immaterial, the source of all causal power, etc. doesn’t need to do that and indeed cannot intelligibly be said to do it.
As I see it, the problem with merely telling the dust to become a man is that it under-specifies the effect – or in philosophical jargon, under-determines it. (What kind of man is the dust supposed to become? A tall one or a short one? Brown eyes or blue? A Will Smith lookalike or a Tom Cruise replica? Blood type A, B, AB or O? Exactly how many cells should this individual have? What sequence of bases should he have in his DNA?) And since dust, by itself, is unable to make a choice between alternatives – even a random one – then nothing at all will get done, if God commands dust to simply become a man. In order for God to generate a real man, every single detail in the man’s anatomy has to be specified, right down to the atomic level, and not even a Deity can make a man without specifying these details.
In short: making a living thing properly requires making it with a nested hierarchy of organization, in which its components and sub-components are specified in detail, right down to the level of the cell and its constituent molecules. But this is a structural nested hierarchy. What we still need to explain is why living things also exhibit a taxonomic hierarchy.
The programming of life
Professor Daniel Koshland Jr. (1920-2007), who was the editor of the leading US science journal, Science, from 1985 to 1995, listed seven essential properties of living things in a widely cited article entitled, The Seven Pillars of Life. The first of these properties is a program:
The first pillar of life is a Program. By program I mean an organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time. For the living systems we observe on Earth, this program is implemented by the DNA that encodes the genes of Earth’s organisms and that is replicated from generation to generation, with small changes but always with the overall plan intact. The genes in turn encode for chemicals — the proteins, nucleic acids, etc. — that carry out the reactions in living systems. It is in the DNA that the program is summarized and maintained for life on Earth.
I should point out that Darwinian biologists do not envisage the genetic program we find in each organism as a product of design. That is because they typically envisage design in purely top-down terms, along the lines of a blueprint, and a genetic program isn’t like that, as Professor Richard Dawkins points out in his best-selling book, The Greatest Show on Earth (Transworld Publishers, London, Black Swan edition, 2010. There is a significant difference between a blueprint and an embryo’s developmental program: a blueprint is a planned form of architecture, whereas the embryo is characterized by a feature called self-assembly. Blueprints are “top-down” designs – they don’t assemble themselves into houses. However, embryos do assemble themselves into mature humans. Dawkins goes on to say that self-assembly is achieved through “bottom-up” as opposed to “top-down” architecture: “The beautifully ‘designed’ body emerges as a consequence of rules being locally obeyed by individual cells, with no reference to anything that could be called an overall global plan.” (Dawkins, 2010, p. 220.) Thus there is “no overall plan of development, no blueprint, no architect’s plan, no architect” (2010, p. 247) in the rules governing the development of the embryo.
But if we imagine living things as having been originally designed from the bottom up, then the Darwinian objection to genetic programs being products of Intelligent Design is rendered null and void at one stroke. I have argued above that if living things were originally designed, then they must have been designed in this “bottom-up” fashion.
One scientist who has worked hard to build a link between the biological sciences and information technology is Dr. Don Johnson, author of Programming of Life and Probability’s Nature and Nature’s Probability: A Call to Scientific Integrity. Dr. Johnson has both a Ph.D. in chemistry and a Ph.D. in computer and information sciences. He has spent 20 years teaching in universities in Wisconsin, Minnesota, California, and Europe. On April 8, 2010, Dr. Johnson gave a presentation entitled Bioinformatics: The Information in Life for the University of North Carolina Wilmington chapter of the Association for Computer Machinery. Dr. Johnson’s presentation is now on-line here. Both the talk and accompanying handout notes can be accessed from Dr. Johnson’s Web page. Here’s an excerpt from his presentation blurb:
Each cell of an organism has millions of interacting computers reading and processing digital information using algorithmic digital programs and digital codes to communicate and translate information.
On a slide entitled “Information Systems In Life,” Dr. Johnson points out that:
- the genetic system is a pre-existing operating system;
- the specific genetic program (genome) is an application;
- the native language has a codon-based encryption system;
- the codes are read by enzyme computers with their own operating system;
- each enzyme’s output is to another operating system in a ribosome;
- codes are decrypted and output to tRNA computers;
- each codon-specified amino acid is transported to a protein construction site; and
- in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.
The reason why I have described the programming and code of living things at some length is that there is no known unguided process in the natural world which is capable of generating digital codes, let alone programs. Intelligent Design is the only causally adequate process that can create codes and programs. And if these are an essential feature of cells, then it is reasonable to infer that the first cell was designed.
“Cell or cells?” I hear KeithS ask. “How does all this relate to common descent? And how what does it have to do with the nested taxonomic hierarchy that organisms of every kind belong to?”
In order to answer these questions, I’d like to look at two taxonomic levels: the phylum and the class.
The major taxonomic ranks. Image courtesy of Wikipedia.
I’ll start with phyla. The animal kingdom is divided into 40 or so major groups, called phyla; while plants are divided into a dozen or so divisions (which are equivalent to phyla). Other kinds of organisms – including bacteria – have also been classified into phyla. Currently, there is a vigorous and ongoing debate in the scientific community as to whether a phylum should be defined morphologically or phylogenetically. However, a definition of phylum based on an organism’s body plan has recently been championed by paleontologists Graham Budd and Soren Jensen, who are both thorough-going evolutionists. This essentialist account of phyla has the dual advantage of being intellectually elegant and easy to understand, as Professor Michael Behe, a biochemist and noted Intelligent Design proponent, argues in his book, The Edge of Evolution” (2008, Free Press, paperback edition, p. 197):
Animals are divided into a number of groups according to their general “body plan.” For example, one group of animals, chordates (which includes vertebrates like us), have a nerve chord arranged in the back of their bodies, whereas arthropods, the group that includes insects and crustaceans, have a nerve chord in the front. Biologists count dozens of fundamentally different body plans. Types of animals that have the same body plan are generally grouped together in the same phylum, which is the biological classification right under kingdom (kingdom divides organisms into bacteria, plants, animals, and a few other categories).
Since an animal’s body plan is the product of programs operating within the developing embryo (including not only the genetic program but also the epigenetic program), it follows that the taxonomic division of organisms into different phyla reflects the underlying design of the developmental programs that generate these organisms. Each phylum that we find in Nature can thus be regarded as a distinct and well-defined variation of the underlying developmental program.
The next taxonomic level below the level of phylum is that of the class. For instance, cartilaginous fish, bony fish, amphibians, reptiles, birds and mammals are classes which belong in the phylum of chordates (Chordates). In his book, The Edge of Evolution, Professor Behe points out that these vertebrate classes differ in the number of distinct cell types they have: “Although amphibians have about 150 cell types and birds about 200, mammals have about 250” (2008, Free Press, paperback edition, p. 199). Each cell type is quite distinct from the other types in its group. For instance, the cells of the mammary, lacrimal and ceruminous glands share the property of being specialized for secretion through ducts (exocrine secretion), but the substances they secrete are very different: milk, tears and ear wax respectively. Professor Behe argues that the gene regulatory network that is required to specify each cell type is irreducibly complex, and he estimates that the number of protein factors involved in the gene regulatory network for each cell type is about ten. There is an old Chinese proverb that a picture is worth a thousand words, and it’s certainly true in this case. Readers who want to see what a gene regulatory network looks like for a tissue type called endomesoderm, in simple sea urchins, can click here. It’s well worth having a look at. The resemblance to a logic circuit is striking, and the impression of design overwhelming.
Behe concludes that the cell types that characterize a class of organisms are very likely to be designed (ibid., pp. 198-199).
Additionally, we may also conclude that if classes are characterized by their own unique cell types, then classes are objective natural categories, with sharply defined boundaries. Moreover, because the different cell types we find in a living organism are all generated by a single gene regulatory network, we can speak of them all as being “variations on the same theme.”
To sum up: we would expect a taxonomic nested hierarchy in organisms which are generated by developmental programs, whose variations at key junctures are what is ultimately responsible for living things falling into different taxa (or categories). If living things are put together in this way, then both the taxonomic hierarchy and the structural hierarchy which are found in living things are features that we would expect life to exhibit.
Russian matryoshka dolls. Each doll is encompassed inside another until the smallest one is reached. This is the concept of nesting. When the concept is applied to sets, the resulting ordering is a nested hierarchy. Image courtesy of Wikipedia.
Before I address the question of common descent, I’d like to close with a short but relevant excerpt from the Wikipedia article on Hierarchy:
A nested hierarchy or inclusion hierarchy is a hierarchical ordering of nested sets. The concept of nesting is exemplified in Russian matryoshka dolls. Each doll is encompassed by another doll, all the way to the outer doll. The outer doll holds all of the inner dolls, the next outer doll holds all the remaining inner dolls, and so on…
A containment hierarchy is a direct extrapolation of the nested hierarchy concept. All of the ordered sets are still nested, but every set must be “strict” — no two sets can be identical. The shapes example above can be modified to demonstrate this:
Square < Quadrilateral < Polygon < Shape
The notation "x < y" means "x is a subset of y but is not equal to y."
Two types of containment hierarchies are the subsumptive containment hierarchy and the compositional containment hierarchy. A subsumptive hierarchy "subsumes" its children, and a compositional hierarchy is "composed" of its children. A hierarchy can also be both subsumptive and compositional.
A compositional containment hierarchy is an ordering of the parts that make up a system — the system is "composed" of these parts. Most engineered structures, whether natural or artificial, can be broken down in this manner.
The compositional hierarchy that every person encounters at every moment is the hierarchy of life.
I submit that if most engineered structures embody a compositional containment hierarchy, then surely the default expectation for intelligently designed life on Earth is that it would embody such a hierarchy, too.
Evidence for common descent
The reader might be wondering why I continue to accept the evidence for common descent, since I’ve just refuted the most powerful argument in its favor: the existence of a taxonomic nested hierarchy which all organisms can be grouped into. My reply is that it isn’t the evidence from hierarchy theory, DNA similarities, comparative anatomy, or embryology that persuades me of the truth of common descent. The alternative theory (put forward by Richard Owen, among others) that living things were created according to certain archetypes in the Mind of the Designer of Nature could explain these things equally well. I am considerably more impressed by fossil evidence showing, for instance, that the first fully aquatic whales (Basilosaurus and Dorudon) had an intermediate-sized vestigial pelvis and rear limb bones, suggesting that their ancestors lived on land. Although one might reasonably object that the vast majority of fossils don’t show any evidence for common descent, the few that do are very striking: it is remarkable that Archaeopteryx, the oldest universally accepted fossil bird, had twenty bones in its tail, like reptiles, instead of six, as modern birds do. But it is the evidence of atavisms (or “throw-backs”), and anatomical and molecular vestiges in organisms that constitutes, to my mind, the most powerful argument for common descent. Here is how Dr. Theobald presents the argument in his essay, 29+ Evidences for Macroevolution:
Skeleton of a Baleen whale circling the hind limbs and pelvic structure. Some baleen whales actually have visible hindlimbs. Some even have feet with toes on them. Image courtesy of Azcolvin429 and Wikipedia.
Probably the most well known case of atavism is found in the whales. According to the standard phylogenetic tree, whales are known to be the descendants of terrestrial mammals that had hindlimbs. Thus, we expect the possibility that rare mutant whales might occasionally develop atavistic hindlimbs. In fact, there are many cases where whales have been found with rudimentary atavistic hindlimbs in the wild (see Figure 2.2.1; for reviews see Berzin 1972, pp. 65-67 and Hall 1984, pp. 90-93). Hindlimbs have been found in baleen whales (Sleptsov 1939), humpback whales (Andrews 1921) and in many specimens of sperm whales (Abel 1908; Berzin 1972, p. 66; Nemoto 1963; Ogawa and Kamiya 1957; Zembskii and Berzin 1961). Most of these examples are of whales with femurs, tibia, and fibulae; however, some even include feet with complete digits…
A vestige is defined, independently of evolutionary theory, as a
reduced and rudimentary structure compared to the same complex structure in other organisms. Vestigial characters, if functional, perform relatively simple, minor, or inessential functions using structures that were clearly designed for other complex purposes. Though many vestigial organs have no function, complete non-functionality is not a requirement for vestigiality…
For example, wings are very complex anatomical structures specifically adapted for powered flight, yet ostriches have flightless wings. The vestigial wings of ostriches may be used for relatively simple functions, such as balance during running and courtship displays — a situation akin to hammering tacks with a computer keyboard. The specific complexity of the ostrich wing indicates a function which it does not perform, and it performs functions incommensurate with its complexity. Ostrich wings are not vestigial because they are useless structures per se, nor are they vestigial simply because they have different functions compared to wings in other birds. Rather, what defines ostrich wings as vestigial is that they are rudimentary wings which are useless as wings.
There are many examples of rudimentary and nonfunctional vestigial characters carried by organisms, and these can very often be explained in terms of evolutionary histories. For example, from independent phylogenetic evidence, snakes are known to be the descendants of four-legged reptiles. Most pythons (which are legless snakes) carry vestigial pelvises hidden beneath their skin (Cohn 2001; Cohn and Tickle 1999). The vestigial pelvis in pythons is not attached to vertebrae (as is the normal case in most vertebrates), and it simply floats in the abdominal cavity. Some lizards carry rudimentary, vestigial legs underneath their skin, undetectable from the outside (Raynaud and Kan 1992).
Snakes may occasionally have vestigial legs or arms, but they should never be found with small, vestigial wings….
Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent. Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous retroviral sequences. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a DNA copy of their own viral genome and insert it into their host’s genome. If this happens to a germ line cell (i.e. the sperm or egg cells) the retroviral DNA will be inherited by descendants of the host. Again, this process is rare and fairly random, so finding retrogenes in identical chromosomal positions of two different species indicates common ancestry.
Dr. Theobald goes on to point out that there are at least seven different known instances of common retrogene insertions between chimps and humans.
It has been suggested that target-site preferences account for the shared distributions of endogenous retroviruses, but the main problem with this suggestion (so I have been told by a competent biologist) is that they are nowhere near locus specific enough to do so. Even if they were, one would still need to explain:
(a) the shared orientations of orthologous ERVs;
(b) the nested hierarchical distribution of ERVs within primate genomes (in particular, the distribution of similarities and differences); and
(c) the striking correlation between the distribution of ERV placement and that of point mutations in env, gag, and pol genes.
The biological function of ERVs has little relevance to the argument for common ancestry. Target-site duplication is the hallmark of insertion, regardless of whether the inserts are functional or not. In any case, it is doubtful whether there is a single known case of an entire ERV which is functional. Instead, what scientists typically find is that it is particular ERV components that are functional, rather than the entire sequence.
In brief: there appears to be good circumstantial evidence for the common descent of living organisms, even if we leave aside the evidence of the nested taxonomic hierarchy which the various kinds of organisms can be grouped into, as well as the pervasive genetic, anatomical and embryological similarities between the different kinds of living things.
Is common descent a natural prediction of Intelligent Design Theory?
(i) Why an old earth?
First, I’d like to propose e two fairly obvious reasons why an Intelligent Designer would not have wanted complex animals to appear instantaneously, on the early Earth.
An artist’s conception of how the planet Mars could be terraformed. Four stages of development are depicted. Image courtesy of Daein Ballard and Wikipedia.
(a) Terra-forming. Complex animals have their own specialized physiological needs, to support their uniquely active way of life. Some changes in the Earth’s environment may have been required before complex animals could appear. For instance, recent research suggests that volcanically active mid-ocean ridges caused a massive and sudden surge of the calcium concentration in the oceans, making it possible for marine organisms to build skeletons and hard body parts for the first time. (See Xavier Fernandez-Busquets, Andre Kornig, Iwona Bucior, Max M. Burger, and Dario Anselmetti. Self-Recognition and Ca2+-Dependent Carbohydrate-Carbohydrate Cell Adhesion Provide Clues to the Cambrian Explosion. Molecular Biology and Evolution, 2009; 26 (11): 2551.) Geological transformations take time to attain chemical equilibrium. Lest anyone think that this calcium upsurge “explains” the Cambrian explosion: it should be borne in mind that a necessary condition is not the same as a sufficient condition. Calcium upsurges don’t explain how hierarchical patterns of protein regulation suddenly arose in animals from that time.
(b) Ecological engineering. The appearance of complex animals would have added to the complexity of ecosystems. There would have been an increase in the number of needs that the first bilaterian animals had to meet, as complex ecological interactions developed. (See Marshall, C.R. (2006). Explaining the Cambrian “Explosion” of Animals. Annual Review of Earth and Planetary Sciences, Vol. 34: 355-384. DOI: 10.1146/annurev.earth.33.031504.103001. ) It takes time to set up a self-sustaining food chain. Once again: ecological explanations of the Cambrian explosion are well suited to explaining why there had to have been a rapid increase in both disparity and diversity, but by themselves, they cannot explain why the “explosion” happened when it did. Nor can they explain how hierarchical patterns of protein regulation suddenly arose in animals from that time.
(ii) Why common descent?
Next, I’d like to suggest that the Designer’s modus operandi can be described by what might be called an Economy of Effort Principle. Very roughly, it states that out of all the possible sets of mutually compatible intelligent and sentient life-forms that the Designer could have made, the Designer will choose to make that set of intelligent and sentient life-forms which is the easiest for Him to produce, and that He will produce the life-forms belonging to that set in the simplest manner possible, where the terms “easy” and “simple” refer to the total length of the assembly instructions for all species.
The separate creation of each and every kind of creature is one way of generating sentient and sapient life-forms, but because these life-forms share many of their genes, there’s bound to be a lot of duplication in their descriptions. If we accept special creation, then the assembly instructions for each species will have to be specified separately, because each species is created separately. Hence the recipe which provides a complete description of all the actions performed by the Designer in designing all species will be unnecessarily long, thereby violating the Economy of Effort principle.
Many people think that front-loading would be the most economical way for an Intelligent Designer to produce intelligent and sentient life-forms. They argue that the Creator should be able to make a universe that can generate life automatically, without Him needing to “fix” or “adjust” it. But that assumption may be wrong. Recently, physicist Robert Sheldon wrote a thought-provoking article entitled, The Front-Loading Fiction (July 1, 2009), in which he critiqued the assumptions underlying “front-loading.”
In the first place, the clockwork universe of Laplacean determinism (the idea that you can control the outcomes you get, by controlling the laws and the initial conditions) won’t work:
First quantum mechanics, and then chaos-theory has basically destroyed it, since no amount of precision can control the outcome far in the future. (The exponential nature of the precision required to predetermine the outcome exceeds the information storage of the medium.) (Emphasis mine – VJT.)
As far as I know, no-one in the “theistic evolution” camp has addressed this basic point raised by Dr. Sheldon. Even today, one still commonly hears objections to Intelligent Design like the following: “Wouldn’t it be more elegant of God to design a universe in which the laws of Nature would generate life automatically?” as if that were a genuine possibility.
In the second place, what Dr. Sheldon calls “Turing-determinism” – the modern notion that God could use an algorithm or program to design all the forms we observe in Nature – fares no better:
Turing-determinism is incapable of describing biological evolution, for at least three reasons: Turing’s proof of the indeterminacy of feedback; the inability to keep data and code separate as required for Turing-determinacy; and the inexplicable existence of biological fractals within a Turing-determined system.
Specifically, Dr. Sheldon argues that the only kind of universe that could be pre-programmed to produce specific results without fail and without the need for further input would be a very boring, sterile one, without any kind of feedback, real-world contingency or fractals. However, such a universe would necessarily be devoid of any kind of organic life. Dr. Sheldon proposes that God is indeed a “God of the gaps” – an incessantly active “hands-on” Deity Who continually maintains the universe at every possible scale of time and space, in order that it can support life. Such a role, far from diminishing God, actually enhances His Agency.
The conclusion we have reached, then, is that the common descent of living organisms is a reasonable (if not compelling) prediction, from an Intelligent Design perspective. Front-loading probably won’t do the trick: it seems that there is still too much “hands-on” work that a Designer would need to do, to generate complex sentient and sapient life-forms.
Creation or evolution? It depends on how you look at it
But the fascinating conclusion that the latest research is pointing to is that from a formal perspective, each species of living thing can be viewed as a creation in its own right, notwithstanding its common ancestry with other species at a material level.
In a recent post, The Edge of Evolution?, I drew readers’ attention to a 2011 paper by the Croatian biochemist Dr. Branko Kozulic, titled, Proteins and Genes, Singletons and Species, which argues that the presence of not one but literally hundreds of chemically unique proteins in each species is an event beyond the reach of chance, and that since these proteins exhibit specified complexity (as the amino acids which make up the polypeptide chain need to be in the correct order), each species must therefore be the result of intelligent planning. (A parallel argument can be made for de novo protein-coding genes.) I also discussed some possible implications of Dr. Kozulic’s research in a follow-up post titled, Some testable predictions entailed by Dr. Kozulic’s model of Intelligent Design.
What the new research suggests is that regardless of whether species are linked by a common family tree or not, a lot of engineering must have gone into the design of each and every species. Literally hundreds of chemically unique proteins and genes must have been designed for each and every kind of living thing on Earth, genetic and anatomical similarities notwithstanding. All of this renders the 150-year-old dispute over creation vs. common descent rather moot. The singular fact that needs to be explained is the evidence of careful planning that we see in the design of living things.
The wrong map?
In his article, KeithS likens Intelligent design proponents to people wandering around with inaccurate maps of the world, leading them to falsely claim that some paths cannot be traversed when in fact they can. In response, I would argue that the truth is the other way round. It is the Darwinists who have the wrong map.
The Intelligent Design argument I’ll be putting forward here is a very simple one. In a nutshell, my argument is all about proteins. Proteins perform very specific functions within the cell. What’s more, living things need lots of proteins: the simplest living cell needs at least 250 proteins; the molecular machines within the cell require dozens of proteins each; the first eukaryotic cell (i.e. a cell having a nucleus, as cells in animals, plants, fungi and protists do) requires hundreds more proteins than a simple bacterial cell; and the new cell types which appeared in the bodies of complex animals required layers upon layers of protein regulation, in a hierarchical system of control. However, as far as we can tell, the odds of even a single protein forming by blind processes (chance plus necessity) are astronomically low: well below 1 in 10 to the power of 150. That’s so rare that you wouldn’t expect it to happen even once, in the lifetime of the observable universe. Short of positing a supernatural act, the only way to narrow those odds is to suppose that either the starting conditions of the universe were rigged, or the laws of Nature are somehow rigged in ways unknown to us, so as to favor the evolution of proteins. But it takes an intelligent being to rig things like that, so we’re back with a Designer.
My Intelligent Design argument can be formulated on six levels, as there are at least six kinds of functional specificity in living things that point to their having been intelligently designed:
(1) Proteins. Every living thing on this planet contains proteins, which are made up of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism. They’re involved in practically all biological processes. To fulfil their tasks, proteins need to be folded into a complicated three-dimensional structure. Proteins can tolerate slight changes in their amino acid sequences, but a single change of the wrong kind can render them incapable of folding up, and hence, totally incapable of doing any kind of useful work within the cell. That’s why not every amino-acid sequence represents a protein: only one that can fold up properly and perform a useful function within the cell can be called a protein. Now let’s consider a protein made up of 150 amino acids – which is a fairly modest length. If we compare the number of 150-amino-acid sequences that correspond to some sort of functional protein to the total number of possible 150-amino-acid sequences, we find that only a tiny proportion of possible amino acid sequences are capable of performing a function of any kind. The vast majority of amino-acid sequences are good for nothing. So, what proportion are we talking about here? An astronomically low proportion: 1 in 10 to the power of 74, according to work done by Dr. Douglas Axe. When we add the requirement that a protein has to be made up of amino acids that are either all left-handed or all right-handed, and when we finally add the requirement that the amino acids have to be held together by peptide bonds, we find that only 1 in 10 to the power of 164 amino-acid sequences of that length are suitable proteins. 1 in 10 to the power of 164 is 1 in 1 followed by 164 zeroes. The Earth has been around for 4,500,000,000 years, but it should be obvious to the reader that that’s nowhere near enough time for a protein to form as a result of unguided natural processes. To get round this difficulty, scientists have hypothesized that maybe Nature has a hidden bias that makes proteins more likely to form, but all the evidence suggests there isn’t any such bias – and even if there were one, that would need explaining too. Finally, scientists have suggested that maybe another molecule – RNA – formed first, and proteins came later, but the same problem arises for RNA: the vast majority of possible sequences are non-functional, and only an astronomically tiny proportion work.
(2) The simplest living cell. Even a minimally complex cell needs at least 250 proteins, for it to work. If the odds of generating even one protein by blind processes during the 4.5-billion-year history of the Earth are astronomically low, then the odds of generating a living cell are much, much worse. To get round this difficulty, some scientists have hypothesized that the first living things didn’t contain proteins: they used RNA instead. But as we saw above, the same problem arises for RNA: only an astronomically tiny proportion of possible sequences can do any useful work, so the chances of a useful RNA molecule forming are very, very low. To get round these astronomical odds, other scientists have proposed that the first living things were made up of something shorter: polypeptides, or TNA. But polypeptides and TNA aren’t alive: even if they could replicate, they can’t evolve. What’s more, all the living things we know of contain very long digital code sequences. For instance, the DNA letters of the genome of the simplest free-living organism – Mycoplasma genitalium – would span 147 pages, if they were printed in 10 point font. So the hypothesis that the first living things were much shorter than they were today is unsupported by any evidence. Finally, some scientists have proposed that the first living things were made of something more exotic than DNA or RNA – maybe clay crystals. But once again, that’s pure supposition, which isn’t backed up by any hard evidence.
(3) Molecular machines. Most cellular functions are executed by complexes containing multiple proteins. These proteins work together in sync, acting like molecular machines. A molecular machine is an assemblage of parts that transmit energy from one to another in a predetermined manner. In living things – even the simplest ones – these machines are each composed of dozens or even hundreds of protein components. If the odds of generating even one functional protein by blind processes are astronomically low, the odds of making a molecular machine are unimaginably low. Some scientists have argued that these molecular machines may have once been simpler, on the grounds that some of the proteins in these machines appear to have been derived from other ones. That’s true, but even when you take out the derived proteins that came along later, you’re still stuck with machines that have dozens or even hundreds of components. So the problem remains.
(4) Eukaryotic cells. Plants, animals, fungi, slime moulds, protozoa and algae are all made up of eukaryotic cells. A eukaryotic cell is like a miniature factory. The cell nucleus contains a multitude of robot-like machines working in synchrony, which shuttle a huge range of products and raw materials along conduits leading to and from the various assembly plants in the outer parts of the cell. Everything is precisely choreographed. A eukaryotic cell exhibits features such as quality control, feedback systems and automated parcel processing (“zip codes”). What’s more, each cell has to be capable of replicating its entire structure within just a few hours. To do all these things, a eukaryotic cell requires thousands of different kinds of proteins. Some scientists have proposed that eukaryotic cells formed gradually in a step-by-step process called endosymbiosis, where one smaller organism came to live inside another, and it’s true that some parts of the eukaryotic cell, such as mitochondria and chloroplasts, seem to have arisen that way. But that doesn’t explain the origin of the nucleus of the cell, which is where most of the DNA resides. A nucleus requires hundreds of different kinds of proteins for it to do its work: an evolutionist’s nightmare.
(5) Animals with complex body plans (e.g. arthropods, annelid worms, molluscs, echinoderms and chordates, as opposed to simple animals like sponges and coelenterates). Complex animals need more cell types in order to perform their diverse functions. New cell types require many new and specialized proteins. But these new proteins also have to be organized into new, hierarchically ordered systems within the cell. That’s because in complex animals, new cell types need to be organized into new tissues, organs, and body parts, which in turn have to be organized to form body plans. In other words, complex animals embody hierarchically organized systems of lower-level parts within a functional whole. So we’re not only talking about lots of proteins, we’re talking about proteins organized into hierarchical levels of control. Once again, no evolutionist has put forward a quantifiable model of how these levels of control might have arisen.
(6) Species. As we have seen, each species of living thing turns out to have literally hundreds of chemically unique proteins. Once again, this is a specified event beyond the reach of chance, forcing us to conclude that each and every species must have been designed.
The evidence for Intelligent Design stems from an attribute of life which is even more fundamental than the taxonomic hierarchy that organisms belong to – namely, the high degree of functional specified complexity we find in living things. It is this singular fact which Darwinists have shown themselves utterly unable to account for, and which leads me to conclude that Darwinism is a failure as an explanation of life, in all its glorious diversity.
108 Replies to “Is Darwinism a better explanation of life than Intelligent Design?”
Quick question. Do you think that there are species that do not fit into a nested heirarchy, and if so, does one example falsify common descent, or would it have to be a critical mass of samples?
An interesting, patient step by step exercise.
In my own summary answer, I would say, that OOL and OO major body plans are both replete with FSCO/I. There is but one empirically warranted adequate source for such, design.
That key gap blows up a major plank of the claims being made.
Similarly, mosaic animals such as the Platypus point to code libraries and inheritance in the object sense.
In the end all the sound and fury over taxonomic trees imagined to traverse a vast continent of function falters on want of key transitionals in the root and main branches, as well as failure to account for FSCO/I on the claimed mechanism.
There is no warrant to ground the claim that the record of life forms we have, fossil and current, has an empirically warranted, blind watchmaker explanation.
So, what is being made so much of, in the end amounts to a distraction, in blunt terms, a red herring.
Until KS et al step up to the crease and convincingly knock a few fours and sixes, they have not got a start for a good innings.
Mathematics fills biology from the dendrology of trees and blood vessels following mathematical formulae, as just one example. Then why think that we be concerned that Markov chains and processes seem to present a problem. Just as particle physics and cosmology yields many mathematical expressions of reality there is this math of life. God’s reality speaks in many mathemaatical ways and Einstein wondered why that was. Those of us who believe don’t have the necessity of wonder.
The message once again confirmed by mutations is the formula of Genesis chapter 1: Living things reproduce only “according to their kinds.” The reason is that the genetic code stops a plant or an animal from moving too far from the average. There can be great variety (as can be seen, for example, among humans, cats or dogs) but not so much that one living thing could change into another. Every experiment ever conducted with mutations proves this. Also proved is the law of biogenesis, that life comes only from preexisting life, and that the parent organism and its offspring are of the same “kind.” Much the same observation is made in Science magazine: “Species do indeed have a capacity to undergo minor modifications in their physical and other characteristics, but this is limited and with a longer perspective it is reflected in an oscillation about a mean [average].” So, then, what is inherited by living things is not the possibility of continued change but instead (1) stability and (2) limited ranges of variation.
An Army can be placed into a nested hierarchy. The US Army is. So that alone refutes the cliam that only branching evolutionary processes produce a nested hierarchy.
Also Dr Denton pointed out in “Evolution: A Theory in Crisis”, gradual evolution requires a smooth blending of defining characteristics. For example, gradiations of reptile-like mammals until they become mammal-like reptiles and finally mammals. You would expect overlapping as opposed to nice distinct sets.
That said, Linnean taxonomy, ie the observed nested hierarchy (even Theobald uses it), is based on a Common Design, and has nothing to do with evolution.
And finally all nested hierarchies are man-made constructs. They are only evidence for our cleverness and nothing more.
(BTW even Theobald, who keiths cites, says his evidence has nothing to do with any mechanism, yet keiths is using it to support unguided evolution.)
Summativity- in order to be a nested hierarchy the scheme must exhibit summativity. That is why any given organism can be laid out in a nested hierarchy- as long as the parts = the whole. Then there are the defining of sets and levels to contend with.
Why did you cite ‘whale legs’ again?
An Email Exchange Regarding “Vestigial Legs”, Pelvic Bones, in Whales by Jim Pamplin
Excerpt: The pelvic bones (supposed Vestigial Legs) of whales serve as attachments for the musculature associated with the penis in males and its homologue, the clitoris, in females. The muscle involved is known as the ischiocavernosus and is quite a powerful muscle in males. It serves as a retractor muscle for the penis in copulation and probably provides the base for lateral movements of the penis. The mechanisms of penile motion are not well understood in whales. The penis seems to be capable of a lot of independent motion, much like the trunk of an elephant. How much of this is mediated by the ischiocavernosus is not known.
In females the anatomical parts are smaller and more diffuse. I would imagine that there is something homologous to the perineal muscles in man and tetrapods, which affect the entire pelvic area – the clitoris, vagina and anus.
The pelvic rudiments also serve as origins for the ischiocaudalis muscle, which is a ventral muscle that inserts on the tips of the chevron bones of the spinal column and acts to flex the tail in normal locomotion.
here’s the entire E-Mail exchange:
Episode IV in the 1984 PBS mini-series Voyage of the Mimi, (still shown to public school students) has a young Ben Affleck visiting paleontologist Dr. Whitmore at the Smithsonian Institute’s Natural History Museum, to get the low down on whale evolution. Affleck is skeptical when the scientist tells him whales evolved from land animals, but is finally convinced by the overwhelming “evidence”. After showing young Ben some marine mammal skulls, Whitmore takes him to a catwalk near the ceiling of a hanging Gray Whale skeleton display. “Pelvic bones” are seen suspended from the ceiling by thin cables, unattached to any other bones of the skeleton. Ben comments,
“Finally, Dr. Whitmore showed me something that really convinced me: pelvic bones. We have pelvic bones. All animals that walk have pelvic bones. The pelvis is where the hind legs attach to the body. Some whales, like this Gray, still have pelvic bones, even though the bones don’t have any purpose now. There wouldn’t be any reason to ever have a pelvis if you didn’t ever have hind legs. And there wouldn’t be any reason to have hind legs if you didn’t want to walk on land.”
Watching this program raised a question in my mind. If these bones are not attached to the backbone, what holds them in place? Bones are normally anchor points for skeletal muscle. What muscles, if any, attach to these bones? To find an answer, I went to Google.com and typed in “Ask a cetologist.” I selected a website from the search results and asked the following:
What muscles are attached to the “pelvic” bones of whales? What are such muscles attached to at their other end? What function do the muscles serve? Are they used for reproduction?
Thank you in advance for any information and sources you might be able to share.
On June 10, 2003 I received the following reply from:
Phillip J. Clapham, Ph.D.,
Large Whale Biology Program
Northeast Fisheries Science Center
166 Water Street
Woods Hole, MA 025434, U.S.A.
tel. 508 495-2316
fax 508 495-2066
I’m forwarding this to an anatomy expert, Jim Mead at Smithsonian…
Wednesday, June 11, 2003, I received the following reply from:
James G. Mead, Ph.D.
Curator of Marine Mammals, MRC 108
National Museum of Natural History
P.O. Box 37012
Washington, DC 20013-7012
(202) 786-2979 fax
The pelvic bones of whales serve as attachments for the musculature associated with the penis in males and its homologue, the clitoris, in females. The muscle involved is known as the ischiocavernosus and is quite a powerful muscle in males. It serves as a retractor muscle for the penis in copulation and probably provides the base for lateral movements of the penis. The mechanisms of penile motion are not well understood in whales. The penis seems to be capable of a lot of independent motion, much like the trunk of an elephant. How much of this is mediated by the ischiocavernosus is not known.
In females the anatomical parts are smaller and more diffuse. I would imagine that there is something homologous to the perineal muscles in man and tetrapods, which affect the entire pelvic area – the clitoris, vagina and anus.
The pelvic rudiments also serve as origins for the ischiocaudalis muscle, which is a ventral muscle that inserts on the tips of the chevron bones of the spinal column and acts to flex the tail in normal locomotion.
The only anatomical works on the pelvis that I known of are in large whales and as follows:
Abel, Othenio 1908 Die Morpholgie der Huftbeinrudimente der Cetaceen. Denkshriften – Osterreichische Akademie der Wissenshaften, Mathematisch – Naturwissenshaftliche Klasse, Wein, 81:139-195.
Arvy, L. 1976 Some Critical Remarks on the Subject of the Cetacean ‘Girdles’. Investigations on Cetacea, 7:179 -186,
Avry, L. 1979 The Abdominal Bones of Cetaceans. Investigations on Catacea, 10:215-227.
Hosakawa, H. 1951 On the pelvic cartilages of the Balaenoptera-foetuses, with remarks on the specifical and sexual difference. Scientific Reports of the Whales Research Institute, 5:5-15.
Howell, A. B. 1930 Aquatic Mammals. Charles C Thomas, Publisher, Baltimore, xii + 338 pp. [p. 302 – 309 deal with the pelvic limb in cetacea].
Lonnberg, E. 1910 The pelvic bones of some cetacea. Arkiv fo”r Zoologi, 7(10) :1-15.
Schulte, H. von W. 1916 Anatomy of a fetus of Balaenoptera borealis. Memoirs of the American Museum of Natural History, new series, 1 (6) : 389-502, pls xliii-lvii.
Struthers, J. 1881 On the bones, articulations and muscles of the rudimentary hind-limb of the Greenland right-whale (Balaena mysticetus). Journal of Anatomy and physiology, 5:141-176 (bones and joints), 301-321 (muscles), pls. XIV-XVII.
Struthers, J. 1889 Memoir on the anatomy of the humback whale Megatera longimana. Maclachlan and Stewart, Edinburgh, [iv] + 188 = , 6 pls. Reprinted from the Jouranl of Anatomy and Physiology, 1887-89.
Turner, W. 1870 On the sternum and ossa innominata of the Longniddry whale. Journal of Anatomy and Physiology, 4:271, ill.
Good luck with your inquiries.
James G. Mead, Ph.D.
Curator of Marine Mammals, MRC 108
National Museum of Natural History
P.O. Box 37012
Washington, DC 20013-7012
(202) 786-2979 fax
Theobald cites car features as something that cannot be put into a unique nested hierarchy. But for what it’s worth, there are two artificial processes that have been demonstrated to produce nested hierarchies. (And of course, I don’t have the links to the research handy at the moment.)
– Journal article citations, and
– Patent citations.
So, it’s not just unguided natural processes that can do it.
I wonder about languages as well. Obviously language can be constructed and modified and influenced by outside languages, but I wonder if the vast majority of language history is characterized by a nested hierarchy.
Like BA I am a little mystified as to why you would choose whales as your example of ‘common descent’, especially Basilosaurus and Durodon.
Nearly every study I have looked at over the years have all agreed on one thing, neither of those are related to the modern day whale, in other words they are thought to have been ‘evolutionary dead ends’.
Can I ask you to provide a paper/study/evidence to the contrary.
Things that Evos Don’t Understand- Unguided Evolution is NOT Compatible with Common Descent
For starters unguided evolution can’t explain how prokaryotes evolved into eukaryotes. It cannot explain how single-celled eukaryotes evolved into metazoans and it definitely cannot explain meosis, without which metazoans cannot reproduce. No reproduction, no common descent.
What unguided evolution is compatible with is genetic entropy, disease and deformaties.
And BTW we do not observe an objective nested hierarchy wrt prokaryotes, so by keiths’ “logic” unguided evolution is falsified (he sez unguided evolution predicts an objective nested hierarchy)….
Dr Torley, as with ‘whale legs’, I find your reliance on ERV’s to support common descent to be highly questionable and not nearly as strong in its conclusion as I’ve come to expect from your research. The reason why I find it highly questionable is because as Dr. Sternberg points out here,,,
The reason why this is a severe problem for common descent (whether Theistic or darwinian) is because ERV’s, at least some classes of ERV’s, are buried deep in the developmental program of an organism. Dr. Nelson points out why this is extremely problematic for any gradualistic process here:
The fact that developmental programs are vastly different between species is substantiated by the recent finding of very different ‘alternative splicing codes’ between species:
As pointed out before, installing a regulatory ‘alternative splicing’ code is a all or nothing, ‘top down’, take it or leave it, deal. And that is what makes this particular piece of evidence so devastating for neo-Darwinists (or even for Theistic evolutionists who believe in common descent)!
In addition, the poly-constraint that poly-functionality places on any conceivable scenario of gradually changing one species into another species, in a ‘bottom up’ fashion, is good to remember:
Poly-Functional Complexity equals Poly-Constrained Complexity
The primary problem that poly-functional complexity presents for neo-Darwinism, or even Theistic Evolutionists is this:
To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study, and further studies, has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained by poly-functionality, I will use a puzzle:
If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome of say 500 interdependent genes, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their falsified genetic reductionism scenario I might add, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford.
This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center).
As to Theistic Evolutionists, who believe God guides evolution incrementally, all I ask you to consider is do you think that it would be easier for God to incrementally change the polyfunctional genome of an organism into another organism, maintaining functionality all the time, in a bottom up manner, or do you think it would be easier for Him to design each kind of organism in a top down manner? The evidence clearly indicates ‘top-down’ design of eack kind of species.
Too funny- Alan Fox thinks VJT’s ID argument is one from incredulity, even thiugh it is an argument based on knowledge borne from observations, experimentation and experiences. And he doesn’t realize that his is an argument from total ignorance.
He also doesn’t understand that saying living organisms are designed is a complete game changer wrt scientific investigation- even Dawkins recognizies that fact.
And Alan sez there isn’t any argument for ID in what VJT wrote. Willful ignorance is your name, Alan.
Maybe, someday, one of teh TSZ ilk or some other evo will produce testable hypotheses for unguided evolution so we could actually compare that to what ID offers.
I wouldn’t hold my breath though…
To show you how clueless Alan Fox is, he actually cites this Pallen & Matzke paper as evidence that refutes Behe’s IC.
Obvioulsy Alan never read the paper because it does not demonstrate unguided evolution can produce any bacterial flagellum. There isn’t any experiments except to show protein similarities which they automatically equate with homology.
“They” say that your argument for ID wrt proteins has been refuted here, somewhere.
One thing I am interested in is the set of things God can not do:
This is not an empty set because the Word says God can not lie about his essential character or his purpose ( Heb 6:18 ) ( At least that is what I assume are the two immutable things in which it was impossible for Him to lie ).
But what I hear from Keith_S is: I refuse to believe that guided evolution would cause nested hierarchies because it is ridiculous to believe that out of all the ways God could have created life, he would have chosen nested heirarchies.
What I hear from you is: Once God chose to build living things in a certain way ( bottom-up construction, reproduction by information encapsulated in DNA) , He could only continue in a way that requires nested hierarchies to appear.
So the argument of Keith_S vanishes. It is no longer ridiculous to believe that the designer built things one certain way out of many, but it is a requirement that once he started a certain way, He must continue in that direction.
Is that a fair statement of, if not your argument, a logical conclusion from it?
vjtorley, thanks for another extensive and well-researched article. Regarding underdetermination you wrote,
I think this is an excellent point. Of course whatever God commands can come about, but that does not suggest that he takes no care with the details, or that there is no need of them. God says to Job,
“Where were you when I laid the earth’s foundation? Tell me if you understand. Who marked off its dimensions? Surely you know! Who stretched a measuring line across it, on what were its footings set, or who laid its cornerstone, when the morning stars sang together and all the angels shouted for joy. Who shut up the sea behind doors when it burst forth from the womb, when I made the clouds its blanket and wrapped it in thick darkness, when I fixed limits for it and set its doors and bars in place, when I said, ‘This far you may come and no farther, here is where your proud waves halt.'” — Job 38
There we see both things occurring, the issuing of commands and specifying their form, albeit poetically. This seems to be the modus operandi of the Father, Son, and Holy Spirit relationship. God’s will issues forth from the Father, it is proclaimed by the Son, and carried out by the Holy Spirit. I think this relationship between aspects of the Trinity with regard to divine causation has some support in the New Testament. So I think it’s possible that all that God does in creation has this model of will, command, and execution. In this regard the Son ties God’s will to his acts, in the issuing of the Word. “Through Him all things were made. Without Him nothing was made which has been made.”
This is an excellent article and Dr. Torley makes several excellent points. I do, however, want to point one aspect of this from the summary of KeithS post mentioned in the first paragraph of the OP.
I find the argument that “the probability of an Intelligent Designer choosing to make living things in a way that mimics unguided Darwinian evolution is very, very low” rather telling. In effect, the critic is employing yet another version of “God wouldn’t have done it that way, ergo evolution”. Just because the possibilities and options available to the designer were wide and varied, it does not follow that the designer had to make a different choice than what we see before us. The claim that it is somehow deceptive of the designer to choose a course that “mimicks” unguided Darwinian evolution. The implication of that notion is that unguided evolution actually works as advertised. And since whether or not that is the case is the point of KeithS’s post, there’s a bit of question begging going on here. There’s also a sneaking in of the theological premise of “God wouldn’t have done it that way.” Perhaps KeithS might demonstrate scientifically how he knows what the designer did or didn’t do.
The other problem with the entire line of argument KeithS is making is that just because we have 2 possible explanations for a given observation, nested heirarchies in this case, one being the purely unguided natural one of Darwinian evolution, and the other being a process created and/or guided by an intelligence (presumably a supernatural one) why is it necessary to choose between them and/or give preference to the naturalistic explanation. What is the scientific rationale for the choice and the preference? Other than mere a priori philosophical prejudice in play, I see no scientific basis for that conclusion at all.
Dr Torley writes:
This reminds of an old joke. An evolutionary biologist met up with God one day and said, “Well, God, we’ve really progresses in our scientific understanding of how life came to be on our planet. In fact, we’ve progressed so much, we now create life from scratch.” “Really?”, replies God, “show me!” So, the scientist reaches down and scoops up a handful of dirt to begin. “Stop!”, says God, “Go get your own dirt!”
Actually Michael Denton convincingly argued that Nested Hierarchies can be used to argue against macro evolution. If the fish are always fish, then they will never be mammals, hence mammals don’t evolve from fish. If one insists the markov chain will have limits on what evolves such that fish will alway be fish, then they will never be mammals!
Denton relates the problem that the transformed cladists made for the Darwinists. One can, just by looking at traits, assemble them into nice nested hierarachies. Yeah, they look at first like they decended conceptually from a common ancestor, but the problem is they all look like siblings and the conceptual ancestor in principle looks like it cannot exist even in principle.
Common Ancestor of Vertebrates and Invertebrates? Err, crash…hard to conceive of even in principle. It’s like looking for a square circle. Those gene sequence worshippers argue the genes show there was a common ancestor of vertebrates and invertebrates, but they seem to have problem describing anatomically what it would look like. Google “common ancestor of vertabrates and invertebrates” and try to find even a hypothetical description of what the common ancestor could look like even in principle. Maybe the lack of transitionals suggest there wasn’t one.
How about about the transitional links from single cell to multi-cellular organisms. The smallest known multicellulars are perhaps 300 cells. Yes its true, a creature like a human develops from 1 single cell in the womb, but that’s not the same as evolution, that’s development. We have a nesting between multicellular and single cellular, and the gap is substantial (we don’t have 2-cell, 3-cell, 4-cell adults)…
Transitionals from single cell to multicell adults seem dubious propositions, much less do we expect to find them. The problem of Irreducible complexity shows up again.
Theobald is a good man, but to say that nested hierarchies are created by evolution presumes that’s the only reason a nested hierarchy exists. Some of it may be based on engineering principles — i.e. there aren’t any 1.5 wheeled vehicles, there are 2-wheeled, 3-wheeled, 4-wheeled vehicles. There is a nested hierarchy automatically by necessity, not by Markov process, in that case.
But, even then, nested hierarchies can be created without and appeal to necessity…for example we have in classical music: concertos and symphonies and sonatas and operas — all were contrivances that are obeyed only by convention. The nesting is natural even though, in principle, it can and does have some violation, the conventios are followed by the intelligent designers (humans).
So I don’t agree that nested hierachies are evidence of common ancestry, the nesting actually suggests the opposite, and Denton highlights how Darwinsits had to change their tune and embrace Linnaean taxony when for the longest time Linnaean taxonmy was evidence against common ancestry. They’ve managed to distort the facts — nested hierachies suggest fish will always be fish — they will never evolve to become eagles, bats, humans, or kangaroos.
Dawkins alluded to the problem of nesting in BlindWatchmaker when he went on a tirade against transformed cladists — his disdain for them is well found since transformed cladists unwittingly provide evidence against Darwinism.
DonaldM @24, indeed, there is no implication of a mechanism whatsoever in the observation of a nested hierarchy. At best it provides the basis for an inference to a historical relationship between all living things. (Joe reminds us at #5 that Theobald steers clear of implicating a mechanism here.)
Even then, it’s not clear to me that a nested hierarchy necessitates a universal common ancestor. At best it would strongly suggest some type of limited common descent. Would not multiple starting points still produce a nested hierarchy, if we merely presumed a universal relationship.
Dr Torley, the whale example really is not good enough as evidence.
As for what we call common descent, I find it reasonable to conclude that it was designed in such a manner to have a workable and sustainable food chain. Will a food chain work if every single biological system was unique?
It’s not clear that this is the case. A developmental program which can accommodate the transformations from one distinct form to another might in actuality be far more complex and effort-inducing than producing unique forms discretely. One can imagine that a program which allows for the transformation of a bicycle into a bulldozer through viable intermediate stages would require far more code specification and planning than producing each independently. Each stage of transformation would require code and planning that would be unique to the stage, and not required by either independent form, even though there might be construction processes and systems similar in both.
Additionally, a distinction needs to be made between common design principles and their actualization. I can reuse design patterns and even the code based upon them, and gain a substantial reuse benefit, even if such files and libraries require physical duplication and instantiation into separate projects. In other words, design concepts are readily reusable even if code or code files are duplicated. This is true for algorithms, libraries, frameworks, and so on. They can be designed once and implemented multiple times, and with modification. So just because discrete forms might have code in common, reuse of the principles of the shared design is what saves effort.
Perhaps there is another way to look at Economy of Effort, but I’m not finding it easy to imagine how creating distinct forms uniquely is less economical than producing an entire developmental framework which accommodates all known forms and their innumerable intermediates.
I’d also like to point out that this type of gradualism is not very robustly supported in the fossil record. While there may be some forms that can be reckoned as intermediates to others, it seems to be the case that sudden appearance followed by relative stasis is the rule rather than the exception. If the designer is creating new forms by directly modifying existing ones, then it would follow that hopeful monsters are being produced at these stages, and not the very slight and innumerable intermediate transitions demanded by gradualism. While this scenario is rather frightful, its inelegance is not evidence against the proposition. However there are other considerations. If intermediate stages between, for instance, land animals and aquatic ones are not infinitesimally small and innumerably abundant, then there’s another issue here. Different forms might necessitate disparate embryological developmental pathways, and this might be logistically infeasible. They would likely also require specific, well-defined symbiotic relationships between fetus and mother that would likely differ from the normal case, requiring a good deal of special case systems and programming. Nursing mechanics and methods after giving birth would also be an issue here. How can such transitions be made, and are they even feasible, and would this represent a more parsimonious approach to design than the alternatives?
The main problem with whales evolving from land animals is that the concept cannot be tested. For example no one knows how many mutations it would take, nor what genes were affected. Heck no one even knows what makes a whale a whale. Evos think that a whale just emerges once the right DNA sequence and expression pattern are archieved.
Again I refer you to Lenski who has demonstrated evolutionary processes have severe limitations. Over 50,000 generations and no evidence for macroevolution. Perhaps if no one was watching as evolutionary processes take on magical powers when no one is watching, then perhaps the E. coli would do something macroevolutionary.
So people who accept universal common descent have some explainin’ to do, because when put to the test accumulations of mutations just doesn’t cut it.
“….. Hence the recipe which provides a complete description of all the actions performed by the Designer in designing all species will be unnecessarily long, thereby violating the Economy of Effort principle.”
Economy of Effort is a redundant principle for our omnipotent God, and wouldn’t be a consideration, vjtorley; at least in the sense that it would be all one to him, however many objects and processes he had to oversee. He might, in some scenarios, prefer ‘to take the scenic route’, on a whim.
He can micromanage the smallest entities in creation, simultaneously, on autopilot, i.e. without his conscious attention; as we, by our autonomic intelligence, breathe, for example, or focus our eyes to take in various aspects of our personal environment.
However, He might be able to do so perfectly consciously while doing every thing else, without getting too bored. On the other hand, since we are made in his image, at least on a minuscule scale, I’m inclined to doubt He wouldn’t get bored. You’ve seen the workings of one amoeba, you’ve seen the lot!
Sorry about my otiose and pedantic longueur in my second paragraph, vjt. Trying to teach a scholar the meaning of such words, as ‘autopilot’!
I started a separate thread on nested hierarchies. One doesn’t have to accept ID to reject Darwinism as an explanation for nested hierarchies. I provided links describing the work of transformed cladists.
Why in the heck would we think this?
Sorry, I sneezed and hit the wrong key causing my comment #34 to post before I was done. 🙂
I know lots of designers. It is quite common for them to make things that they feel are interesting, or unique, or expressive, or demonstrative of their handiwork, etc. The idea that, as a general principle, a “designer will choose to make that set of [forms] which is the easiest” to make is absurd.
Having chosen to make a particular form, a designer might well implement that form using pre-existing techniques and materials and protocols. So in the actual production or implementation, a designer may indeed generally try to do things the easy way, rather than the hard way. But the idea that a designer would only choose to make forms that are the easiest to make is completely unsupported philosophy, in addition to being contrary to many of our known experiences.
Thanks very much for your very thoughtful responses. I’ll be very busy today, but I hope to respond to some of your comments in about 18 hours. Cheers.
Again I feel that I have to congratulate you for your wonderful work. Thank you.
I think I have no comments, because I essentially agree with everything you say here. And I am happy that the protein argument is receiving the correct attention: in spite of some technical complexity, which can make it “difficult” for those who do not have a biological background, it is indeed IMO the most powerful argument for ID, at present. Darwinists’ “objections” to it are really weak and sometimes frankly desperate.
There is no doubt that there are, in the cell and in living beings, all kinds of functional complexity that can, and will, be analyzed to prove design, some of them certainly much more complex than simple proteins and simple protein networks. But a single functional proteins is such an obvious, easy to analyze, product of design that we should really concentrate on that aspect, at least as a first step.
First, I question whether God really did make things in a way that truly mimics unguided Darwinian evolution. I think this interpretation is simply forced upon the evidence both where it fits and does not fit.
Secondly, I understand what you are saying here, but from a creationist perspective, I think he has a point. I think we CAN say that God would not have done it like that. Why? Because He told us in His Word that He did not do it like that.
As Barb said in post #4, nested hierarchies fit well with the creationist idea that God created all living creatures “according to their kinds”. There was a lot of possibility for variation within the kind, but evolution beyond the “kind” barrier would be impossible.
Chance said this in post #27
I agree. I think it fits nicely with what God does tell us about creation in the Bible.
I was disappointed to see Meyer and Torley come out so strong in support of common descent!
Of course God COULD have done it that way, but, if He tells us something different, why reject that and instead insist He used common descent?
Is anyone really going to read the Bible and think, “Oh, common descent!” No. That is why no one believed that until Darwin came along. It is obvious that we are simply reading something into Scripture that isn’t there. The most obvious problem this interpretation has is that the order of creation is different than the supposed order of evolution. First comes the plants on Day 3 and then on Day 5 you have fish and birds.
(I guess you could also add the sun, moon, & stars on day 4 as a problem for big bang cosmology, but I know the pat answer that they just appeared on earth on day 4. I guess that means they were hidden for millions and millions of years while the plants were supposed to have evolved? Or maybe we can add some more ad hoc and make the days overlapping?)
I guess in the end, I’m with Keith S. I do not think God would have created like that. I don’t think He would have used death, competition, suffering, disease, trial and error, and mutations as a means of creating the perfect world that Genesis 1 describes. Not only would that be out of character for a good, loving God, but it disagrees with His Word. He clearly told us that He did NOT do it that way. So I base my opinion, not on what I personally think or on what 21st century scientists think might have happened in the distant unobservable unrepeatable past, but on what the Creator Himself tells us in His Word.
Just my 2 cents. I enjoy the discussion though, even though I don’t agree with everything. And I appreciate the fact that even us science denying creationists are allowed on this board.
The perfect creation story is unbiblical
Very much liked your analysis in the link @ 39 and I agree that insisting the “‘good’ creation meant no plant or animal death” gets in the way of sound Biblical exegesis, but I would add one caveat. “Known unto God are all His works from the beginning.” (Acts 15:18) The need for suffering and death in the creation could always be because of the sin of man. God’s decisions even if they seem contingent are not bound by time.
I’m glad you like it and I hope the argument on my blog makes sense.
I would like to add and I make it clear in my article, that it is through pain, suffering and death that God displayed His glory to us. Without those there could not have been a resurrection and John makes it clear in his Gospel;
“Through Him all things were made; without Him nothing was made that has been made.”
I’ve finally got time for a few quick responses to comments on my post. Here goes.
A number of readers asked why I found the arguments for common ancestry so convincing. I don’t wish to get into an argument here, so I’ll confine my remarks to one creature: the snake. I suggest that readers have a look at the following articles:
Najash rionegrina, a snake with legs by P.Z. Myers
Najash (Wikipedia article)
Oldest snake fossil shows a bit of leg (New Scientist, 19 April 2006)
Snakes Evolved on Land, New Fossil Find Suggests (National Geographic, 19 April 2006)
Evolution Of Snakes (Lenny Flank; talks about rapid bursts in the evolution of snakes which I would say were intelligently designed)
The Evolution of Snakes (2009 article)
Snake Evolution – Photos of Vestigial Hind Limbs on Snakes (Ed Babinski)
The Evolution of Snakes (A creationist take on the whole matter)
The picture of a snake with atavistic legs here speaks volumes. I think that atavisms, plus the evidence from vestigial pelvis remnants in boas and pythons, and the recent discovery of fossil Cretaceous snakes with legs attached to their pelvises, is enough to show beyond reasonable doubt that snakes are descended from creatures that had legs, about 100 million years ago. What it does not show is that snakes evolved through undirected processes, as Darwinists mistakenly contend. In fact, Lenny Flank’s article provides excellent reasons to think that a Darwinist account of snake evolution is deficient.
The Easy Way?
Eric Anderson, while agreeing with my point that designers generally make things the easy way, asks why I think God would have generated those intelligent and sentient life-forms that were easiest to make. Maybe He didn’t; but what I’d suggest is that if the creation of intelligent and sentient life was His over-riding aim, then the default assumption would be (a) that He’d go for the process that enabled Him to realize His goals with a minimum of effort; (b) that He’d go for the life-forms that were the easiest to produce, in conformity with His plan. I admit (b) is somewhat more questionable than (a) in that God may have had other goals, but even (a) by itself would be enough to justify common descent. It avoids unnecessary duplication, that’s all.
Biblical Evidence for creationism
I don’t consider myself a Scripture scholar. However, I’d argue that the Biblical statement that God made every living creature according to its kind is compatible with the kind of protein engineering process I described in my post above. In any case, it seems that if you’re going to accept a plain literal reading of Genesis, the verse you really have to watch out for is this one:
” For in six days the Lord made the heavens and the earth, the sea, and all that is in them, but he rested on the seventh day. Therefore the Lord blessed the Sabbath day and made it holy.” (Exodus 20:11)
Sal Cordova writes:
I would respectfully disagree with Denton here. It’s important to get the names right. The name of the higher nested hierarchies that mammals belong to are: amniotes (not reptiles), tetrapods (not amphibians) and vertebrates (not fish). We’re still vertebrates, even if we’re not fish.
Got to go now. I’ll be back in a few hours.
The snake would be a case of losing something. Universal common descent requires the addition of many parts.
Spot on!!! No new body plans and only a loss of existing parts. Same can be said for speciation , it occurs due to a loss of information not because of any gains.
Very good answers, again.
I understand that the point of common descent is very controversial here, so I feel that I have the duty to state, for the nth time, that I do accept common descent for exactly the same reasons as you do. I agree with with that nested hierarchies are not the best argument for CD.
I have never cared much for fossils, not because they are not important, but because they are not my field, and because I do prefer to reason in molecular and digital terms. So, my best argument for CD are the homologies between proteins with similar functions, IOWs the homologies of sequence in the context of basci protein domains, or lower branches of the proteome.
I do believe that CD is at present the best explanation for that huge aspect of data. I sincerely doubt that those homologies, including, but certainly not limited to, ERV insertions, can universally be explained by functional restraints. The reason is very simple. We certainly know that not everything in protein sequences is indispensable to function, otherwise the functional space for each function would be made of only one sequence. That is certainly not the case. And still, huge homologies in sequence can be found throughout the proteome, and many of them cannot be explained in terms of strict functional necessity, as far as I can understand from data.
So, the best explanation remains CD, and as I am committed to accepting the best explanation, I do accept CD, for exactly the same reasons why I accept ID and not neo darwinism.
I understand that many here think differently, and I am always ready to change my mind if and when data will suggest a different explanation, according to my judgement.
I respect the reasons people accept common descent, and to my mind, I’m glad a large segment of those in the ID community are not creationists.
But I had to take issue with KeithS claim:
KeithS equivocates the notion of nested hierarchy. We have a nested hierarchy that is phylogenetic (like a family tree) and another that is taxonomic (like the way we perceive biology in terms of platonic types). The taxonomic platonic nested hierachy is not predicted by evolution, and actually a naturalistic mindless process will not create a platonic nested hierarchy even though it can generate a phylogenetic nested hierarchy.
Like most Darwinists, KeithS, equivocates and conflates taxonomic nested hierarchies with phylogenetic nested hierarchies to prove a claim, but equivocations are no proof whatsoever!
You might look at some of the later comments I posted in the separate thread on how it is empiricallly evident the taxonimic nested hierarchy that is constructed by looking at taxonomic traits is at complete variance with the phylogenetic nested hierarchy constructed by the prevailing notions of how mammals evolved from fish. One can provisionally accept Common Descent and conclude that the taxonomic nested hierachy is at complete variance with the predicted phylogenetic hierarchy. Denton was correct to point out that the persistence of certain diagnostic characters that define things like mammals is actually the antithesis of Darwinisn and supports strongly the PRE-Darwinian conception of platonic forms in biology versus mindless accidents. Platonic forms expressed in biology implies Intelligent Design.
Darwinists have successfully equivocated phylogenetic nested hierarchies with taxonomic nested hierarchies in public and scientific circles and thus through a process of distortion furthered their undeserved domination of the origins controversy.
By the way, Theobald is making the same equivocations KeithS makes. I don’t think they even realize it!
By the way, Theobald though correct that evolution will create a nested phylogenetic hierchy via a Markov process is completely incorrect to imply that a Markov process will create a nested taxonomic hierarchy. The fact he doesn’t even realize the distinction only shows how lacking in insight the Darwinists are, and it pains me to say it because Theobald is a good guy and accomplished scientist.
I can agree with what you say. Nested hierarchies, however, are not my main interest, and I believe that they prove little, in one sense or in the other. I certainly agree with you that Keith’s argument is flawed, certainly for the position of those who, like me, accept CD, and probably also for the position of those who do not accept it.
Of that last point I am not really completely sure but, as I accept CD for completely different reasons, as I have tried to explain, I am not really interested to that aspect of the debate.
As I have great esteem for you, I would be truly interested to know how you can explain, if you don’t accept CD (do I understand that correctly?), the strong homologies existing between similar proteins in different species. Do you believe that all of that can be explained by functional constraints? (That is, IMO, a very hard argument to support). Or have you different explanations?
Here is a article at Creation evolution headlines that may be of some interest.
Thank you for the kind words. I don’t have explanations for the questions you pose, and I trust the scientific process over time will help us to see which explanation makes more sense. Thus, even though I’m a creationist, you’ve never ever heard me defend it vigorously except perhaps on the question of Origin of Life (which even Darwin asserted in his book Origin of Species, was a created progenitor).
Regarding protein homologies, I wrote more on the other thread how a taxonomic nested hierarchy would resist interpretation as a phylogenetic nested hierarchy. I illustrated it with musical compositions. It would be an interesting exercise in bioinformatics if we could demonstrate the homologies are such that they create a taxonomic hierarchy while at the same time resisting interpretation as a phylogenetic hierarchy. I attempted to do that with the cytochrome-c examples in that other thread, but it probably seems too esoteric for most, so I provided the music illustration to help illustrate the point I was trying to make.
I do not think the strong homologies among species is due to functional constraint, and actually as we see genomes of various species begin to deteriorate via the accumulation of mutations, it will be evident that the homologies are not the result of random process but rather common design.
The illustration of the musical compositions I provided is the best way I can think of in trying to convey this highly esoteric concept of how we can distinguish empirically between phylogenetically generated nested hierarchies versus pre-planned, intelligently designed taxonomic hierarchies. The protein homologies like the “homologies” in the body plans follow a platonic pattern, not one that can even in principle be the result of a Markov process. The question of special creation versus some front loaded design I set aside for later although, if pressed for what I consider an empirical argument, I would point to John Sanford’s Genetic Entropy thesis, which does lead to testable predictions about the future of the human genome.
excellent and timely PeterJ:
And that my friends is a prime example of science done Darwinian style! 🙂
Universal Common Descent may be true but as it stands it ain’t science because it cannot be tested. All we have is circumstantial evidence that can be applied to and supprt other scenarios. AND all experiments demonstrate that prokaryotes give rise to prokaryotes, meaning UCD can’t even get beyond that without invoking gobs of luck. Again that is not science.
Similarities point to a common DESIGN. And the differences point to different design requirements.
As for ervs, please read ERVs not the evidence for UCD you once thought
As a creationist, I do not accept common descent first and foremost for biblical reasons, but those reasons hold little weight for IDers, so for now, I’ll put them aside.(although I believe they are the most powerful arguments of all since the Creator knows better than anyone what He did and did not do.)
However, I do believe there are scientific reasons as well to challenge common descent. The fact that so many IDers actually do struggle with this idea is support for this.
First of all, there is no known Darwinian mechanism that can provide the new genetic information for (for lack of a better word) macroevolution. So evolution beyond the original adaptability that the Creator built into the original kinds is impossible. It does seem like there are boundaries that evolution cannot trespass.
Nested hierarchies can be seen as evidence for common design as well as for common descent so it is not conclusive.
Convergent Evolution raises it’s nasty head all over the place these days and is further evidence against common descent. Convergent evolution is nothing more than a strategy to avoid falsification of common descent.
It is telling though that even Darwinists have trouble concocting a consistent tree of life.
David Coppedge, of JPL Lab fame who lost his job because of passing out ID dvds, wrote this summary of a recent article about Darwin’s Tree of Life.
It is quite shocking!
There is an amazing admission in the original article! They are actually recommending discarding evidence that doesn’t fit with their theory so they can claim the evidence supports their theory.
Gotta read it to believe it. Links to the original article can be found in the article, but here is the damning quote:
But this is not the first time that Darwin’s Tree of Life has been called into question. The evidence does not point to common descent, but rather to a bush with various sprouts.
Other articles reporting on this problem:
Does anyone remember this headline on New Scientist a few years ago?
Darwin Was Wrong: Cutting Down the Tree of Life
That’s all fine and good, but for a theory to be viable it would have to explain all the evidence and not only the evidence in one field. (if it even does that – if it did that, there would be no need to throw out non-conforming data.)
Reasoning in molecular and digital terms is great, but when you reason in other terms, you can come up with a different story. Homology for instance will get you a different tree than using the genome to discern the tree. And neither tree really is consistent anyway.
So now you have scientists that want to ignore the uninformative conflicting data and use only the data that better conforms to their theory.
Well, this got too long.
Food for thought.
And those similarities are easily explained by a common design. Ya see most proteins are used in every day cellular activities. Activities that are very similar so require similar tools and machinery.
What we wouldn’t expect is for a designer to redesign every part of each organism from scratch.
Check the problems these guys are having….
The tree is broken
And Craig Venter said so!
@ PeterJ #48
Sorry PeterJ, I didn’t notice that you already posted the article on crev.info and I reposted it.
I agree with Joe and Andre (@ 43 & 44)
I don’t understand your thinking when you claim that loss of function(in this case, legs in snakes) is evidence for common descent. Wouldn’t the change have to go the other way for it to be true evidence for common descent? This is what creationists want to see – novel organs that are developed from the creation of novel genes by mutation as opposed to just genes switched on/off which means the information was already present.
Perhaps it would be good to familiarize yourself with how creationists and others deal with that.
For instance, here is an article that deals with one of those fossil snakes that had legs.
Here is the summary from the article:
As in my request to Vjt at #11 (for whale evolution, of which I am still awaiting a response), I am interested in what else he would consider a good example within the fossil record for common descent.
The example of the ‘snake with legs’ makes me wonder why evolution would go to the bother. A fish develops legs, walks on land for a while and becames a reptile, loses legs and becomes a snake.
Is that really how people like Vjt envision it?
Trueorigins has a response to Theobald’s 29 evidences for Macroevolution article at this site for those interested:
I haven’t had time to go through it yet. It is a bit old – 2001 I think, but still it probably has some good information.
Why do people at UD reference creationist sites as proof against evolution? Surely, you guys know that no one in mainstream science takes them seriously. I doubt that any credible scientist feels threatened by any of those articles and that the theory is now in jeopardy because of them. Would any of you question Darwinian evolution if the bible didn’t exist? Would you accept the evidence as legitimate and beyond doubt? Todd Wood admits that the evidence is overwhelming but chooses to ignore it in in favor of his faith. THAT IS NOT SCIENCE! Creationists just keep looking for reasons to hold on to their beliefs no matter what the cost instead of being honest with themselves. I used to have faith but not as much anymore because Darwinian evolution seems to be a sure thing.
You need allot more faith in unguided evolution than in design. Firstly you need to explain how matter can just appear, how said matter coul arrange itself and then how such matter came alive, worse still how said matter can think about it. Good luck in your faith, I hope it serves you well.
“Darwinian evolution seems to be a sure thing.”
Really? Perhaps you would care to cite the exact experiment that falsified the following null?
The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
1) Mathematical Logic
2) Algorithmic Optimization
3) Cybernetic Programming
4) Computational Halting
5) Integrated Circuits
6) Organization (e.g. homeostatic optimization far from equilibrium)
7) Material Symbol Systems (e.g. genetics)
8) Any Goal Oriented bona fide system
10) Formal function of any kind
11) Utilitarian work
The Law of Physicodynamic Incompleteness – David L. Abel – August 2011
Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility.
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
Where’s the substantiating evidence for neo-Darwinism?
Why do you attack the messenger and avoid the evidence?
What evidence is overwhelming? Lenski 50,000+ generations and not even a new protein.
Why is it that unguided evolution only does something when no one is looking and there are are eons of time to throw around?
How many generations does it take to get something totally different from the starting population? How many mutations is that?
If you find any Darwinists sites supporting ID, feel free to post. 🙂
Yup, happened to another person we all know:
Shermer says he underwent “deconversion in graduate school six years later when he studied evolutionary biology.”
An alternative account written by Shermer himself:
How We Believe
Atheist Fred Hoyle did, so did agnostic Michael Denton, and their works were the staple of much of what became the modern ID movement, Denton especially. As far as me personally, probably, because Darwinism makes little sense empirically and theoretically, it is supported with illogic misinterpretation of facts. It’s possible atheism is true and Darwin is wrong, at least that what Atheists Fodor and Piatelli-Palmari asserted in their latest book, “What Darwin Got Wrong”.
By the way, we could include atheist Antony Flew, but after he studied ID, he stopped being an atheist.
Besides the fact Darwinists have no empirical evidence whatsoever that purely Darwinian processes can generate even a single functional protein (whereas IDists do have evidence Intelligence can), What does it even mean in the Darwinian worldview for something to be considered true?
Comprehensibility of the world
Excerpt: ,,,Bottom line: without an absolute Truth, (there would be) no logic, no mathematics, no beings, no knowledge by beings, no science, no comprehensibility of the world whatsoever.
Do the New Atheists Own the Market on Reason? – On the terms of the New Atheists, the very concept of rationality becomes nonsensical – By R. Scott Smith, May 03, 2012
Excerpt: If atheistic evolution by NS were true, we’d be in a beginningless series of interpretations, without any knowledge. Yet, we do know many things. So, naturalism & atheistic evolution by NS are false — non-physical essences exist. But, what’s their best explanation? Being non-physical, it can’t be evolution by NS. Plus, we use our experiences, form concepts and beliefs, and even modify or reject them. Yet, if we’re just physical beings, how could we interact with and use these non-physical things? Perhaps we have non-physical souls too. In all, it seems likely the best explanation for these non-physical things is that there exists a Creator after all.
“It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter”.
J. B. S. Haldane [“When I am dead,” in Possible Worlds: And Other Essays , Chatto and Windus: London, 1932, reprint, p.209.
Sorry for not getting beck to you sooner. I’d like to make some clarifying comments regarding your claim in #11 above that nearly every study you have looked at agrees that neither Basilosaurus nor Dorudon is related to the modern day whale, and that both of them are thought to have been ‘evolutionary dead ends’.
1. Even if these fossils were not ancestral to modern day whales, that would not mean that they were not related to modern whales. Your uncle is not your ancestor, but he is certainly your relative.
2. There is no consensus that Dorudon was an evolutionary dead-end, and even Basilosaurus has his staunch defenders as a possible ancestor of modern whales. (All emphases in the quotes below are mine – VJT.) Even the scientific reference you cite as backing up your claim actually appears to believe that Basilosaurus and/or Dorudon may have been ancestral to modern whales. The author writes:
Here’s an excerpt from the Wikipedia article, Evolution of cetaceans:
And here’s a quote from a 2000 article entitled The Origin of Whales and the Power of Independent Evidence by Raymond Sutera, who was personally assisted by Dr. Philip Gingerich in writing the article:
On the other hand, the evogram published by Berkeley University forthrightly declares:
Nevertheless, the evogram depicts Dorudon as the uncle of today’s whales, as it possessed a tail fluke, very small hind legs, and a nasal opening shifted further back than its predecessors. So he was certainly a close relative, at the very least.
You also ask:
Yes, in essence. It sounds like a roundabout way to get to snakes, but along the way, genes and proteins were being acquired by the ancestors of today’s snakes. Making them branch off from other reptiles saved unnecessary duplication of time and effort on the Creator’s part.
You also write:
I mentioned Archaeopteryx above, with 20 bones in his tail, like reptiles (birds have six). If that’s not a good enough example, how about the reptile-to-mammal transition?
Please note that in accepting the reality of such transitions, I am not crediting Darwinian evolution with the capacity to create new structures.
I hope that helps.
Thank you for your posts. You write:
I don’t invoke common descent as a mechanism for evolutionary change. For me, it’s simply a vehicle for the Designer to generate species more efficiently and with a minimum of effort; that’s all. New genes and new organs are the creative work of the Designer, as far as I’m concerned.
You suggest that loss of legs may have occurred after the Fall. However, I’m afraid the fossil evidence suggests that snakes lost their legs tens of millions of years before humans appeared on Earth, and hence long before the Fall of Adam. You can find an interesting article on snake evolution here. Enjoy!
Dr. Torley, perhaps you would be interested in viewing this video which has Dr. Gingerich himself admitting to a fairly embarrassing fact about whale fossils:
Whale Evolution vs. The Actual Fossil Evidence – video
That certainly does not inspire confidence in common descent!:
Whale Evolution? – Exposing The Deception – Dr. Terry Mortenson – video
How Whales Have (NOT) Changed Over 35 Million Years – May 2010
Excerpt: We could have found that the main whale lineages over time each experimented with being large, small and medium-sized and that all the dietary forms appeared throughout their evolution, or that whales started out medium-sized and the largest and smallest ones appeared more recently—but the data show none of that. Instead, we find that the differences today were apparent very early on.
Discovery of “Oldest Fully Aquatic Whale” Fossil Throws a Major Bone into Whale Evolution Story – 2011
Until now, the whale series went something like this:
“Pakicetids (fully terrestrial): ~50 mya
Ambulocetids (semi-aquatic): 49 mya
Remingtonocetids (semi-aquatic): 49 mya
Rodhocetus (a Protocetid, semi-aquatic): 47 mya
Basilosaurids (fully aquatic): 40 mya”
So under the previous timeline, Darwinian biologists didn’t have to worry about accounting for the origin of fully aquatic whales until about 40 mya. This new find pushes fully aquatic whales back to 49 mya. Now the timeline looks something like this:
“Pakicetids (fully terrestrial): ~50 mya
New Fossil Jawbone (fully aquatic whale): 49 mya
Ambulocetids (semi-aquatic): 49 mya
Remingtonocetids (semi-aquatic): 49 mya
Rodhocetus (a Protocetid, semi-aquatic): 47 mya
Basilosaurids (fully aquatic): 40 mya”
In light of this new find, it appears that fully aquatic whales existed at 49 mya — around the same time that Ambulocetids appear. The fossil record now might jump from fully terrestrial Pakicetids to fully aquatic whales in just a couple million years — maybe much less than 5 million years. In fact,
Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology – video
Evolution And Probabilities: A Response to Jason Rosenhouse – August 2011
Excerpt: The equations of population genetics predict that – assuming an effective population size of 100,000 individuals per generation, and a generation turnover time of 5 years – according to Richard Sternberg’s calculations and based on equations of population genetics applied in the Durrett and Schmidt paper, that one may reasonably expect two specific co-ordinated mutations to achieve fixation in the timeframe of around 43.3 million years. When one considers the magnitude of the engineering fete, such a scenario is found to be devoid of credibility.
I’m really unimpressed with your evidence for common descent Dr. Torley, it seems if you really want to make your case then your stuck in the same boat as Theistic Evolutionists and Darwinists in that you would have to show it is possible to change incrementally from one species to another, and I don’t see you even coming close to making your case in that regards!
Thanks for your kind remarks. I am of much the same mind as you are, when it comes to the evidence for common descent – and like you, I would change my mind if I came across a better explanation. A Platonic account seems about the best rival explanation to common descent, to my mind.
Thanks very much for the links. I’m in agreement with you about the impossibility of incremental change from one species to another by undirected processes.
Regarding the 49 million-year-old aquatic whale, I would urge caution. It’s not often that you find the first members of any given species in the fossil record, and if a fossil species goes back X million years, you can be fairly sure its true age is a few million years older than that. The evolutionary transition from land animals to fully aquatic whales could be as short as 4 million years; alternatively, it may be as long as 20 million years.
The 40 million-year-old whale you describe was supposedly a member of the Basilosauridae, according to the team that discovered it. Yet every online reference I can find on the Basilosauridae still lists them as being only 40 million years old, not 49 million (see here and also here, where basilosaurids are said to date from the Bartonian stage of the Eocene, 38.0 to 41.3 million tears ago. The story about the Antarctic find seems to have gone awfully quiet on the Internet since late 2011, and I’m inclined to think it may have been a false alarm. Perhaps the date was wrong; I don’t know.
I don’t disagree with the point that Dr. Sternberg makes in his video. It’s an excellent demonstration of the insufficiency of natural selection to account for whale evolution.
Re: Ba77 @68,
I agree that incremental changes are problematic, as are sudden ones. There is no scenario I can imagine for transforming one complex system into another, either rapidly or gradually, to gain a net advantage in simplicity or efficiency. Such transformations, it seems to me, would need to be exponentially more sophisticated than creating disparate systems individually. The problem is easy to imagine with examples like the one I mentioned up thread. Transforming a bicycle into a bulldozer through intermediate stages would require a significant amount of extra planning over creating each form individually. At each stage the form would need to be viable, and make accommodations specifically for the transformation. In essence, each stage would be a new design, albeit one that could make use of some elements from both the source and destination forms. For instance, the first stage from bicycle to bulldozer might be to replace the wheels with a single track system, integrated into the manual pedal drive, adding all the necessary accommodating modifications, which would be numerous. The next step might be to incorporate a motor to replace the pedal driven system, and this too would require all sorts of unique accommodations specific to this stage. So in order to make such a transformation, each intermediate stage is essentially a unique design, borrowing conceptually from the source and target forms in varying degrees along the way, but also containing a significant number of design accommodations that are only needed by each specific stage. From a human perspective, this is a design nightmare, because each stage needs to be viable and functional, and each stage is, practically speaking, a unique design.
For biological systems the problem is no simpler. At the body plan level we have skeletal morphology, musculature, the central nervous system, the digestive system, and most notably the reproductive systems. At the molecular level there are proteins and metabolism, genetic code, and regulatory code, which is significant with things like micro RNAs and alternative splicing. We also have to account for the entire development process, from single-cell through differentiation and all the stages of embryological development. Each of these systems and processes need to be dealt with specifically in such a way that they accommodate the necessary modifications in all of the other systems and processes. I think it’s practically impossible to imagine how such transitions could simplify the process of design or make it more efficient.
As for common descent, that’s an internal debate of course. Setting aside specific design scenarios that try to account for all the evidence, there’s nothing about common descent that is incompatible with ID. But there are design implications, like the ones I note above. I think for common descent to make real sense from an evidentiary point of view, if it is the practical interpretation of the evidence, we should expect to see it well supported not just in the fossil record, but at all levels of morphology, genetics, and reproduction. As it stands, it seems that similarities in forms, whether body plans or proteins, provide enough that common descent is a logically permissible interpretation, but it’s unclear to me how it could actually be tested. Also, if specific similarities count as evidence in favor of common descent, what counts as evidence against it? What is the objective criteria we use to determine if descent with modification is fully supported by the evidence? And how much of the evidence in favor of common descent would apply to limited common descent as well as the universal version? How many hypothetical common ancestors could be eliminated from a UCA tree without disturbing the empirical evidence?
I agree Chance and good illustration, although I would hold the problem is much more severe because of the exponentially worse constraint that the extreme integrated complexity of life presents above and beyond that which is present in man-made objects. Ironically Eric’c inverse proportion rule seems to be in full force here thus far for Dr. Torley’s explanation as to how it could even be possible to incrementally change one species into another:
a few assorted notes:
Was there a particular post on that blog you had in mind? That’s quite an interesting link so thanks for that, but the tone was fairly upbeat overall so I’m not sure what you were referencing there with that comment?
In any case, I’d be interested to know what the specific story you had in mind was.
For anyone liking Universal Common Descent I invite you to read “Why Is A Fly Not A Horse?” by geneticist Giuseppe Sermonti and then tell me how you feel about the concept.
However I will say this- the only way UCD is even feasible, is by design- intentional and Intelligent Design. However until we know what makes an organism what it is we will never know how to test it.
Chapter VI “Why is a Fly not a horse?” (same as the book’s title)
Bring out the Voles!
Rodent’s bizarre traits deepen mystery of genetics, evolution:
Yup after all this “evolution” a vole is still a vole. This study alone should cast a huge shadow over evolutionism.
In “The Deniable Darwin” David Berlinski puts it this way:
Ba77 @ 72,
“I would hold the problem is much more severe because of the exponentially worse constraint that the extreme integrated complexity of life presents above and beyond that which is present in man-made objects.”
Agreed. Biological systems are astronomically more sophisticated than the examples I cited, so the problem becomes much more difficult even to imagine, much less implement. I also recall Paul Nelson pointing out that perturbations to development are radically destructive, and this complicates scenarios that need to introduce gradual changes. Introducing rapid changes has its own problems I think.
Once we accept design as the best explanation for life and its subsequent development, I think we should examine the feasibility of UCD from a design perspective. Fossil evidence is useful, but skeletal morphology is just a single criteria among many for how organisms might be historically related. Soft biology, as Denton puts it, should be taken into account as well, but that’s not generally possible with fossils. Then there’s the developmental pathway, which is quite significant. If similar forms have different soft biology, or if those forms are generated through different developmental pathways, how justified would an inference to ancestral relation be? Certainly proteins figure in here. If similarities can indicate a possible ancestral relationship, can dissimilarities count against it? And then there’s the regulatory codes. How might we produce an objective standard of evidence here? At some point, I think it makes sense from a design perspective, to raise the bar for what constitutes good evidence for UCD. As it stands, I think that limited common descent is better supported by the evidence, all things considered. Universal common descent appears a bit like an artifact of naturalistic reasoning, in part perhaps necessitated by the extreme low probability of life arising by chance. Using the fossil record as a basis, we have numerous forms appearing suddenly and then remaining relatively unchanged over time in most cases. Accounting for the evidence makes UCD unnecessary, at least as I view it.
Gradualism is unwarranted from a design perspective, and this is supported by the evidence. Specific cases of presumed ancestral relatedness should be evaluated on multiple lines of evidence, with criteria for rejection of the hypothesis being possible in those cases. At best, a design hypothesis which is consistent with fossil evidence looks pretty much like Punctuated Equilibrium, minus the neo-Darwinian mechanism. So for those rapid periods of isolated and unobservable transitions, there needs to be a feasible pathway, otherwise discrete creation events remains the best explanation for what we observe, at least at some biological classification level. Of course phenotypic plasticity also figures in here. Some specimens can accommodate quite different physical traits depending on environmental factors, and this introduces further constraints upon developmental pathways, but may also provide some flexibility relating to how some morphological changes could occur. It seems to me we’re at a point when we can’t be too certain about anything with regard to ancestral relatedness in its universal form. I’d be interested to hear if there are good arguments with regard to physical evidence which provide a basis for accepting universal vs limited common descent. Individual cases, such as land animal to whale and chimp to human events, can be considered on a case-by-case basis. If UCD is true, then those transitions necessarily occurred. Under LCD, the cases are actually debatable.
Apologies for the rambling. I’m trying to manage a flurry of thoughts here.
OT: Animating Bacterial DNA Replication – Jonathan M. – May 16, 2013 – video
Excerpt: This is the kind of thing that, in my opinion, simply screams out “design!”
Even without narration and only background music, DNA replication still screams design
DNA – Replication, Wrapping & Mitosis
Joe @74, good stuff. We have no idea what actually makes these creatures what they are, much less how one might be transformed into another, and whether or not that is possible or plausible.
@75, I’d be curious to know if any of the species of voles come about through differing developmental processes; or if the DNA of one species could be cloned into the egg of another, such as was done with carp and goldfish, and what constraints exist in this sort of cross-species cloning.
Chance and Dr. Torley, you may find this interesting:
Here is a sneak peek at Dr. Meyer’s forthcoming book which may shed a lot more light on this constraint found for body plan plasticity:
Moreover there another whole level of information on a cell’s surface that is scarcely understood:
This following video speaks for itself:
Maybe this will help you
From their website,
I quote from the article…
“But when it is only filled for four percent—the other 96 percent is just air—there is only one conclusion: it is time for more.”
The facts of the tree of life is 96% air? How can 4% be considered good enough evidence that the Tree of life is a fact? A Fact so often sold by our “we believe in unguided evolution crowd”…
But it gets worse of the 4% we do have only 17% of that 4%’s data is available the rest is gone….
But never you mind it is a fact, because Dawkins said so!
The point of the open tree of life project is not a fact. It’s about making the trees underlying scientific papers avaliable as electronic files for anyone that might want to study them.
It’s about data-avaliablity, not conclusions (and you can get the DNA sequences underlying any published paper and run the analyses yourself, so it’s not even about reproducability)
Spare me, the tree has been sold as fact for how long now? Darwin started it and the disciples all have been selling this “fact”.
Here is another disciple defending the indefensible!
Have you ever seen the NCSE’s logo?
Yes! It’s Darwin’s tree sold to the children in school as a fact!
A link from the NCSE’s website
Yes they say its a fact!
Check who is credited!
This site is a collaborative project of the University of California Museum of Paleontology and the National Center for Science Education. For more information, see our credits page.
That there is a tree of life is a fact. We still argue about how to reconstruct it though.
And here is the NCSE Defending the facts of the tree of life!
from the paper linked above!
“The concept of common ancestry is at the
core of evolution. The very idea that
different species arise from previous
forms via descent implies that all living things
share a common ancestral population at some
point in their history. This concept is support-
ed by the fossil record, which shows a history
of lineages changing through time. Because
evolution is the basis for biology, it would be
surprising if any textbook teaching contempo-
rary biology would portray common descent
other than matter-of-factly”
There is no tree…. sigh its a concoction of imagination and metaphysical beliefs, it is not science!
Well, if you have any evidence for that idea let me know.
Thank you for your detailed response to my questions.
The transition between one species into another, in the years that I have been looking into this, is in my opinion the biggest argument against ‘evolution’, ‘common descent’.
I believe on those grounds alone that the lack of any clear transitionals is enough to render the theory of evolution null and void.
What I do find highly interesting, and probably the best argument in favour of ‘evolution, is the supposed transition from reptile to mammal. However, when all is said and done, concerning the similarities between ‘mammal-like-reptiles’ and ‘mammals’, there is still to be shown an actual transition between the two.
Now I don’t believe that can be disputed. Looking over the various resources on this there does appear to be a clear line drawn between the two, either something is a reptile, or it’s a mammal.
And that seems to be the case with every supposed transition offered by science, at least those of which that are often reffered to in the fossil record. For instance we are told of the transition between fish to tetrapod (possibly to some form of amphibian), amphibian to reptile, reptile to dinosaur, reptile to bird, reptile to mammal etc. But in each and every case the fossil evidence that any of those transitions ever took place, as far as I can see, doesn’t actually exist, except perhaps in the eyes of those who wish to see it.
It’s like I have said a hundred times in the past, I visit sites such as this to get to the truth about this matter, and have been doing so for nearly 7 years, but there is this one hurdle that simply defies all efforts to prove it conclusively, and that could be resolved, even somewhat, if a clear example of a transition taking place in the fossil record could be found.
The fossil evidence of evolution, again as far as I am concerned, is problem enough for Common descent, and until something definite is discovered, I don’t see how it will ever be resolved.
Thanks again Vjt, I have really enjoyed this post 🙂
An excellent post VJT. A few comments to add that seem not to have been made so far:
(1) I much appreciated the application of nested heirarchies to ecology, suggesting that, whatever the “system” of creation is, ecology is part of it. This is very much underemphasised on all sides of the discussion. The job spec is not to produce a lot of organisms that work, but a lot of working organisms that work together, for which unguided Darwinian struggle is a totally inadequate explanation.
(2) This relates to your contended idea of God’s choosing the “easiest” method. I share the hesitation of some about God’s need, or desire, to spare his effort – just as I reject entirely the idea that boredom enters into the equation in any way – theistic personalism has, I see, infiltrated ID just as it has theistic evolution, to the detriment of God’s glory.
But whilst it is always dangerous to impute motives to God, it’s true that what is economical in effort is also beautiful in elegance – and the Universe is replete with the truth that God prefers to work in ways that are beautiful. So your ground-up approach can be said to display an aesthetic economy, which seems to me more appropriate to God than the idea of economy of effort.
(3)That said, the theologian in me remains a little unhappy with either “top-down” of “ground up” decriptions of God’s work, for he surely creates holistically – thus the immanent activity you describe in each stage of descent with modification is inherent in the original plan, which is why it’s not “interference” as the TEs say. In that sense, Ed Feser’s (admittedly inadequate) description of God’s creation makes some sense – As God wills the creation of mankind in his image, his intellect conceives every stage necessary to produce him, in his environment, in one all-encompassing view. That, to me, is what a divine Creator is all about!
(4) Lastly, I like your equivocation about whether your description is “evolution” or “creation”, because that genuinely divine guidance of creation through evolution is what the first “TEs” envisaged (eg Asa Gray, Charles Kingsley, or B B Warfield), long before Young Earth Creationism baptized a particular biblical literalism and before modern theistic evolution veered off into its current heterodoxy.
In other words, I think you describe a genuine orthodox via media – congratulations.
Here you go
Do you need more?
Link above should have been http://potiphar.jongarvey.co.u.....evolution/
“Biology currently lacks a robust and comprehensive description of early evolution. We should aim to fill that void, but in a language that operates with biology and chemistry, not with branching patterns in phylogenetic trees, versions of which based on informational genes are called the tree of life. Genomes attest unequivocally to the abundance of lateral gene transfer in microbial chromosome history, but current thinking on early evolution is still largely couched in the conceptual framework of trees. When it comes to getting a fuller grasp of microbial evolution, trees might be standing in the way more than they are actually helping us at the moment, because i) the overall relatedness of prokaryotic genomes is not properly described by any single tree, and ii) the relationship of eukaryotes to prokaryotes is also not tree-like in nature because the endosymbiotic origins of organelles introduces lineage mergers and genetic amalgamation into the evolutionary process.”
so, there is loads of horizontal transfer at the root of the tree, and it’s hard to reconstruct ancient radiations that were relatively rapid. That doesn’t mean the tree is a lie.
It means the tree is wrong. If there is one thing I urge you to do is read this whole paper!
follow the evidence wherever it may lead.
The Dictionary of Life | Origins with Dr. Paul A. Nelson – video
Estimating the size of the bacterial pan-genome – Pascal Lapierre and J. Peter Gogarten – 2008
Excerpt: We have found greater than 139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref.  do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered.
Age doesn’t matter: New genes are as essential as ancient ones – December 2010
Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
Could Chance Arrange the Code for (Just) One Gene?
“our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
That all depends on what you mean by a tree of life. It is not a fact that all living organisms owe their collective common ancestry to some unknown population(s) of prokaryotic-like organisms. That cannot even be tested.
So again it all depends of what you mean by “tree of life”.
Jon Garvey @93,
I think that as long as we are talking about a “designer” in the generic sense, it’s appropriate and even desirable to speak in terms of efficiency and economy. Designers generally operate under constraints. However if we’re speaking theologically, then of course we can dispense with the notion that effort or materials would need to be spared. God may be an engineer, but he is no less an artist.
I couldn’t agree more. C.K. Chesterton puts it this way:
“Now, to put the matter in a popular phrase, it might be true that the sun rises regularly because he never gets tired of rising. His routine might be due, not to a lifelessness, but to a rush of life. The thing I mean can be seen, for instance, in children, when they find some game or joke that they specially enjoy. A child kicks his legs rhythmically through excess, not absence, of life. Because children have abounding vitality, because they are in spirit fierce and free, therefore they want things repeated and unchanged. They always say, “Do it again”; and the grown-up person does it again until he is nearly dead. For grown-up people are not strong enough to exult in monotony. But perhaps God is strong enough to exult in monotony. It is possible that God says every morning, “Do it again” to the sun; and every evening, “Do it again” to the moon. It may not be automatic necessity that makes all daisies alike; it may be that God makes every daisy separately, but has never got tired of making them. It may be that He has the eternal appetite of infancy; for we have sinned and grown old, and our Father is younger than we.” — Orthodoxy, Page 58
It could hardly be said better.
I presume by, infiltrated ID, you mean ID proponents, and not ID methodology, but perhaps not. What do you mean by theistic personalism, and in what way has it infiltrated ID and theistic evolution?
I’ve contested up thread this very idea, that there is any economy whatsoever in a bottom up process which must make transformations between distinct, isolated forms (#29, #71, and some of #77). And I would argue that not only is there a total lack of economy in such a process, due to it’s unfathomable complexity over creating such forms discretely, but there would be no guarantee of any aesthetic benefit either. Where are all of these hypothetical intermediate forms, what would they look like, and whose glory are they proclaiming in their absence? I don’t deny that God could have worked this way, but there is no economy that I can see there; and speaking theologically, there’s no reason to think that this process would be more aesthetically appropriate than distinct and specific creative acts.
By theistic personalism I mean the same as Ed Feser does in quoting Brian Davies, the thing in question being otherwise known as neotheism, and opposed to classical theism. I don’t regard it as intrinsic to ID, but being very a la mode in Evangelicalism nowadays I see its presumptions cropping up here quite often, mainly in off the cuff remarks about the limitations of the designer (which would be fine if a created designer or intrinisc teleology were being seriously proposed).
In current theistic evolution, though, it’s pretty much an essential concept, for from it arises the whole “creation free to create itself,” “self-limiting kenotic God” etc, and TE’s emphasis on theodicy – if there is natural evil, it’s a problem that God has to deal with or be found wanting. Yeuchgh.
I can’t argue with with your disagreement on the economy/aesthetics of “descent with modification” v “direct creation”, in that I’ve never agreed with Darwin’s suggestion that evolution is self-evidently a more glorious view of God: he can create as he please, and the result is just as wonderful in my eyes. However, I do see a particular kind of beauty in an unfolding, progressive mode of creation, and I guess Dr Torley does as well – however my main point was to provide a better alternative to God’s reducing his workload as a motivation.
But one thing coming from VJT’s presentation is that the boundary between truly theistic evolution (as opposed to the modern dog’s breakfaast) and progressive creation can be pretty fuzzy. And personally I don’t see a clear Scriptural case for individual “special” creation, and certainly not for a young earth. But to me the how and when of creation is less important than the recognition of God’s governance of it, in theological terms.
Jon Garvey, thanks for your clarifying remarks. I’ll admit to not being overly concerned with theological hair splitting about whether some theists attribute too much personhood to God, if I can put it so simplistically. While it may be advisable to avoid conceiving of God as being too similar to human persons, I think it’s equally advisable to avoid placing him too far out of reach. After all, the person of Jesus Christ and the nature of the hypostatic union seem to suggest rather strongly that God shares attributes with us, even if by acts of his own will. In John’s gospel, Jesus makes a point of calling his disciples friends, which is a pretty dramatic statement considering the Creator of the universe is speaking. If we attempt to conceive of God as being utterly different from us, then the phrase, made in God’s image, loses all meaning. So perhaps I miss the finer points that Feser is making. I admit to being at best an amateur theologian and armchair philosopher, but audacious enough to make arguments anyway, if only for the purpose of having them supported or refuted.
I agree it’s helpful and necessary to provide a distinction between the common conception of theistic evolution versus Christian Darwinism, which benefits from the equivocation. I admit to having a visceral dislike of the neo-TE theodicies, and their attempts to dictate how God must have acted. I definitely get the inexplicable “icky” feeling when experiencing how today’s brand of theistic evolutionist discusses evolution, Intelligent Design, or their brand of Faith and Science. Eek.
With regard to creation, we all have our preferences it seems. Whatever those are, whether special creation or guided evolution, I’m personally more interested in a) our common support for the concept of intelligent design in nature, which I think is evident to all, and b) what evidence and reason can say with regard to what we observe in biological life and its historical record. In other words, when it comes to ID, I could care less whether ID proponents are YEC, OEC, or support some form of gradual evolution. However when it comes to universal common descent and the mechanisms for gradual evolution, I do have some opinions and I’m comfortable exploring them. I don’t think that UCD is supported in the fossil record, but I do think that some form of limited common descent is quite defensible. I also think there are issues with decent with modification scenarios, when those modifications are supposed to account for transitions between distinct and original forms, and we should explore the various ways this might have occurred. Even trivial specificity seems to be absent whenever guided evolution comes up.
Anyway, thanks again for your thoughtful comments. I’ll spare you further proselytizing. 🙂
I agree with your priorities, and not just because of some intellectual leaning towards design, but because the whole nature of God and our relationship to him depends on it. I like this quote from Charles Kingsley, remembered as an early fan of “Origin of Species” and therefore as a 1st generation TE, who nevertheless said:
That’s the key issue of design – mechanisms are far less of an important matter.
@120 Jon Garvey
Jon, just for clarification, I’m curious as to what you mean by special creation.
Could you explain that to me please?
Oops. That should be @102 not @120.
@87 & 97 wd400
Just a quick question, but if we don’t know how to reconstruct the tree and it the tree differs depending on what criteria you use to reconstruct it, just how do you know that it does in fact exist. How do you know it is a fact?
You mention some of the problems in reconstructing a tree. Then you say “That doesn’t mean the tree is a lie.”
How do you know? Couldn’t one just as easily say “No, but neither does it mean it is true.”?
There is evidence that suggests it is false just as there is evidence that can be used to support it.
The common design argument can explain both the positive and negative evidence much better than the tree of life or UCD hypothesis can in my opinion.
special creation = a created species versus a species that was evolved
The term was used a lot by Darwin. Modern Creationists use the term kind or baramin.
People can split hairs over the what “special creation” means. But Darwin’s usage of the phrase was dishonest in that he said “special creation” = “no variability in the species”, hence all he had to do was demonstrate some variability like he did with the finches and he was thus able to knock down the strawman and pretend he disproved the hypothesis of God’s creation of new species.
Creationists do use it in the way Darwin used it, but for creationists a special creation is a creature that was created that didn’t have ancestors. But it doesn’t mean the created creature can’t evolve (contrary to Darwin’s strawman) See: