The predictive power of evolutionary biology, part 204506
One topic which I plan to address in my blogging is evolutionary biology: its accuracy, its scientific power, and its opponents. In my own research, a critical insight from evolutionary biology underpins the entire theoretical structure of my work. That is the insight that all living organisms are descended from a common ancestor, and that this relatedness can be easily observed. The innumerable observation of this relatedness at many scales of biological organization can is so powerful that we can now use it to predict the organization of biological systems that have not been observed. Many such predictions have been made, and nearly all have been successful. This is what makes a scientific theory powerful: it organizes a large body of facts and provides predictive power about new observations. It is often claimed by those who deny modern evolutionary biology that it is not predictive, but let me be the first to tell you that these flat-earthers are simply ignorant of much of what is going on in modern science.
From the largest organisms to the smallest biological macromolecules, we see homology between organisms. A bat’s closer relation to humanity than birds is easily seen in the structure of the bones of its wings, which resemble the bones of a human hand in number and arrangement, if not size. The skeletal structure of bat wings and human hands are homologous–they are parts of two organisms that are shared with the same part of their common ancestor. Just as the middle finger which types the letters “d”, “e”, “k” and “i” of these words is homologous to the middle finger of innumerable yahoos across the country who raised that finger in traffic this morning, all of our middle fingers are homologous to the inner digit of a deer’s front cloven hoof.
There is homology not only on an anatomical level, but at the molecular level as well. Almost all biological processes in the cell are carried out by protein molecules. Proteins are extremely variable because their properties derive from the sequence of amino acids that constitute them. Proteins can be compared to long strings of gemstones that fold into a given shape because of the interactions between different types of gemstones. These gemstones are the amino acids; in nature there are twenty different amino acids used by nearly all cells to build protein molecules. The sequence of amino acids determines their shape and their function, because the different amino acids have chemical properties that cause them to interact with one another and with their environment in specific ways. The blueprint for these molecules is well-known to be genes which, like paragraphs of a book, are stored in the genome – a large store of DNA in the nucleus of each cell. Protein molecules read each gene and make a copy of it in the form of RNA. This RNA leaves the nucleus and is read by a large protein assembly – the ribosome – to make protein molecules. There is a specified relationship between a bit of DNA sequence and the amino acid that is added to a growing protein molecule, and this relationship is known as the genetic code. The genetic code is virtually identical for every species, but does not follow logically from the laws of physics. This is further evidence that all life evolved from a single common ancestor eons ago.
Like bone structures between bats and primates, there is homology between the same protein molecule found in different species, and there is also homology between different proteins in the same organism. This is further evidence of evolutionary change, and even provides insight into how different genes evolved.
In my own work, I am trying to solve the structure of the biogenic amine transporters. These are small protein molecules at the surface of brain synapses that reuptake neurotransmitters from the synaptic space between two brain cells. By sucking these neurotransmitters from the synapse, neurotransmission is arrested, and drugs used to treat depression such as Prozac work by blocking the transporter protein so that neurotransmission of serotonin occurs over a longer period of time. There are different transporters for different neurotransmitters, and the SSRI drugs such as Prozac work relatively well because they are relatively selective for the serotonin transporter. Drugs like cocaine work because they give you the euphoria associated with blockade of the serotonin transporter but also the addictive qualities associated with blockade of the dopamine transporter (and dopamine neurotransmission is associated with reward-seeking and reinforcing behavior).
The atomic structure of these transporters is unknown, which limits our ability to design drugs with greater specificity and potency (potency in pharmacology is the ability of a drug to cause an effect at very low concentrations). Therefore, a lot of work is being done to find the structure of this transporter and a description, on an atomic level, of how various drugs and neurotransmitters actually interact with the protein. In structural biology, most of the best work is accomplished by means of X-ray diffraction studies. Light microscopes work by focusing light shining through the sample; however, the wavelength the light focused cannot be any bigger, roughly, than the size of the sample under consideration. The size of atoms is smaller than the wavelength of visible light, so normal light microscopy cannot be used to get an image of atomic-sized phenomena. As we know from de Broglie and from quantum physics, electrons do have a wave nature and a wavelength on the order of magnitude of very small objects and even large atoms (such as metal ions). This is the basis of electron microscopy, and it is with electron microscopy that we are able to get vivid pictures of crowds of bacteria on the point of a needle. However, electron microscopy doesn’t allow us to probe smaller atoms such as carbon and oxygen and nitrogen seen in protein molecules. X-rays are, however, small enough. But they cannot be focused, since there is no lens capable of focusing them. However, by shining X-rays at a protein crystal (a crystal being an ordered array of individual molecules, as troop columns are ordered arrays of solders) and applying mathematical operations on the diffraction pattern, we can pinpoint the location in space of every atom in the system larger than hydrogen atoms. In the case of X-ray crystallography, the lens is a mathematical lens rather than a physical one. For this to work, a large sample of the pure protein must be obtained, and it must be crystallizable. Some proteins, unfortunately, have simply not been amenable to crystallization, including many proteins that sit in the oily cell membrane, on cell surfaces – like the biogenic amine transporters.
A major breakthrough a few years ago occurred, however, when a bacterial homologue of the serotonin transporter was successfully crystallized and its structure solved. As a mentioned above, protein molecules have homology just as wings and arms and even skulls do. It turns out that, although bacteria presumably don’t feel depressed, they do have proteins that are related in amino acid sequence and three-dimensional structure to human proteins. This reflects the great conservation in biological evolution of certain families of proteins.
Although it is impossible to know for sure what the structure of the serotonin transporter is without solving its structure, it is possible to generate a model of the protein based on the structure of its homologue. This is possible for two main reasons: (1) the structure of a protein is uniquely determiend by its amino acid sequence, and (2) during evolution, the structure is more stable and changes more slowly the associated sequence, so that minor changes in sequence are allowed which maintain three-dimensional structure. This is for a number of reasons, all of which provide more evidence of biological evolution directed by natural selection. Amino acid changes (mutations) which lead to large structural changes in a functional protein will cause biological defects which limit survival of the organism, while changes which lead to minor changes or which bring about new function will be allowed.
For my problem, I should be able to find the structure of the human serotonin transporter computationally by substituting bacterial amino acids on the structure with the human versions, where they differ, and then performing molecular dynamics simulations on the resulting homology model. These simulations allow the protein to fold up in a virtual physical environment in accordance with the laws of physics and chemistry. This will allow us to generate a model (a theory) of the transporter that can serve to organize our results from pharmacological experiments in which various amino acid residues on the actual human serotonin transporter are mutated to test for their relevance to structure and function. In many experiments, the model has proven to be accurate – by mutating a residue that the model shows is near the binding site of the drug, the activity of the drug is changed, but by mutating residues far from the binding site, activity is unaffected.
I will follow this post with an examination of how we know for sure whether two proteins are related by evolution, or simply arrived by chance at a similar amino acid sequence. But the existence and power of homology modeling itself is an important reminder that insights from evolutionary biology are not only good at explaining the data we have, but are also powerful in allowing us to make predictions about nature.
36 Responses to “The predictive power of evolutionary biology, part 204506”
While I certainly agree that substantial evidence exists for evolutionary biology, I don’t understand why shared characteristics is evidence of it. Just because two creatures contain the same or similar middle finger, it doesn’t followed that they necessarily evolved from a prior, different creature.
Josh,
Evolution as a scientific theory predicts that homology necessarily exists; if there were not common ancestors between organisms, there is no reason to expect any amount of homology.
Huh? Of course there is. Homogeny can be explained by a common creator as much as it can by a common ancestor. There is of course plenty of other evolutionary based evidence but I don’t see why homogey in and of itself is evidence. Creationism would also predict homogeny exists.
Creationism wouldn’t predict that homologous proteins would be lightly modified and put to other uses in other organisms. One would expect an all-powerful creator to come up with the ideal protein, every single time, and not to borrow a protein from one genus over, change a couple of letters of the genetic code, and hope for the best in a totally different function. The latter is what we see, however.
One very plausible explanation for homogeny is certainly evolution, but it isn’t convincing in my mind as the only explanation for homogeny. There are too many other possible explanations as well. I’m not convinced, as Jason argues, that a creator would necessarily come up with an ideal protein, every single time, and not borrow a protein from one genus over. Why would we assume this?
I think that evolution has far too many other more convincing arguments than homogeny in and of itself.
On what basis does creationism predict homology?
Certainly, homology is not incompatible with creationism. We can’t read the mind of the creator, (whichever creator happens to be the flavor of the day) so anything is possible. For the same reason, however, there is nothing from creationism that predicts anything about the type of life that would be created.
Anyway, when did they let Kuntz start posting here? Man, this place has gone downhill fast.
(J/K).
I agree with Josh that homology is just as compatible with creationism (or, more generally, the notion of intelligent design) as it is with evolution. However, Michael is right that since a designer could have re-used certain design aspects throughout the biological world, or could have just as easily made each species totally unique, ID makes no prediction about homology.
Therefore, although homology is compatible with both concepts, it only constitutes evidence for evolution.
Regarding the science in this post, I had one nitpick: X-rays *can* be focused. See here, for example. Whether they can theoretically be focused small enough to image small atoms I do not know, but X-ray diffraction is a much easier way to determine the arrangements of atoms in a crystal.
Also, I presume the biogenic amine transporter you are studying has been sequenced–i.e. you know the order of amino acids in the protein chain, you just don’t know how the chain coils up in 3-dimensional space? And that this is how you’ve determined that the bacterial protein is homologous?
Finally, a plea for temperance–I don’t think it’s helpful to label those who disagree with modern evolutionary biology as “flat-earthers.” While there are some individuals who willingly engage in deception and fraud to try to push their interpretation of the book of Genesis, there are many others who accept evolution as a useful model, yet object to the metaphysical conclusions pushed by a similarly small minority of evolutionists.
Hi Eric, thanks for the information on X-ray focusing. I was originally taught that X-rays cannot be focused by normal lenses. And that is true, but if physicists make progress in focusing X-rays for microscopy, that would be very positive for materials science and possibly molecular biology. I should have been more careful in my statement – X-rays do simply pass through most substances without being refracted, and the key to building a lens is having a material with the right refractive index for the wavelength you’re working with. But there are, of course, telescopes that focus X-rays, and it is with these that we have spotted the signature X-ray emissions from black holes.
I worry about the usefulness for a lot of protein structural biology, though, because the other problem with using a theoretical X-ray microscopy on single macromolecules is that single protein molecules are very weak scatterers of X-rays. Again, most X-rays will pass right through the sample without being diffracted, and those beams that are diffracted will be too weak for detection. That is where crystals come in. We use crystals because they are an ordered array of many single molecules of the sample. The strength of the diffraction pattern of the single molecule is therefore magnified by the number of molecules in the crystal. Crystals will always have imperfections that decrease the resolution, though.
And finally, I apologize for the snark. I didn’t really intend the use of the phrase “flat-earthers” to be an insult so much as an analogy. But it is a poor analogy, since educated people even in ancient Greece accepted that the world was round. A better analogy would be those who opposed the Copernican model of the solar system. Once the scientific community accepted the Copernican model, any educated person who rejected heliocentrism did so not because of the merits of the science behind the model, but out of ideological and religious fear of the implications of the model. It implied to some that humans were no longer at the center of the cosmos, and this possibility was to be opposed on religious grounds. I personally do not care if someone rejects the evolutionary model of biological natural history, but I want to point out that no scientific objection has been successful at providing a different explanation, and most opposition to evolutionary theory now amounts to religious arguments that have nothing to do with science.
Finally, I’ll argue whether similarity implies homology (whether it is the result of common descent or not) in my next post.
And in some future post I’ll lay out my position on the debate between those who believe that modern science is compatible with religion and those who do not believe in this compatibility. My opinion on that deserves a real post, because my opinion on the matter is somewhat complicated (as it should be, because it is a complicated issue).
I’m not convinced, as Jason argues, that a creator would necessarily come up with an ideal protein, every single time, and not borrow a protein from one genus over. Why would we assume this?
Because it ill-befits a Creator to do sloppy work.
And the work is indeed sloppy: At times, the proteins of one organism appear to be poorly transcribed copies of proteins from another organism.
Here’s an example. Unlike most mammals, cats don’t have the ability to taste sugar as sweet — because a big chunk of the relevant gene apparently got deleted in transcription.
A big part — but not all of it. This is suspiciously shoddy work for a Creator, but it’s precisely what we’d expect if speciation happened through a process of selection out of random mutations.
Chuck- sorry for getting to this so late. The existence of homology in anatomical structures reflects an evolutionary process specifically because of instances, as alluded to by Jason with proteins, in which modification of a structure allows an organism to perform a function that is “making the best of a bad solution”. Stephen J. Gould famously used the example of the panda’s ‘thumb’ as the title of one of his books on adaptive processes. Pandas do not have a thumb that is homologous with our thumb- it is not actually a digit. What they have is an elongated radial sesamoid, a bone that normally makes up a section of what we think of as the wrist. The panda’s radial sesamoid can be used to strip leaves from bamboo, though it is a suboptimal solution for this task relative to having an actual thumb. Why not just have a fully opposable, jointed thumb? Pandas have this because they are descended from the common ancestors of bears and raccoons. The non-opposable assembly of five digits had long since been in place- and pandas still have that. At some point, pandas had a mutation in one of the developmental genes that allowed for a misshapen radial sesamoid. Those pandas foraged more efficiently relative to their clumsier relatives, showing that even an unarticulated half-thumb is better than none at all.
But all of this is of little use rhetorically because people whose world view is threatened by the existence of an uncontrolled evolutionary history for Earth’s biosphere will go to great lengths to argue that such phenomena were really just part of the functional “plan”, even in instances where the morphological adaptations in question are clearly traits that made the best of what there was to work with. So. What to do. There is another field of evolutionary biology that has been ignored for far too long (40 years at least). It requires some scholarship and logical/mathematical chops, but is at its core the real smoking gun. It is what made the geological fossil record irrelevant. We must have the public be confronted with the development of Kimura’s neutral theory of molecular evolution, the concept of the molecular clock, and the classic DNA sequence studies that demonstrated that he was right. For everyone who still does not think that multiple descendant forms can derive from single ancestral forms, the evidence for it lies in functionally unconstrained DNA. Silent sites. Those bits where mutations are selectively neutral. They act as a sort of clock, reflecting time since divergence for separate species. I have been re-constructing my collection of classic molecular evolution literature based on what I can remember from Howard Ochman’s class at U of R long ago. I will send it to you.
Oh- and by using the word “ignored”, I do not mean to imply that neutral theory has been ignored scientifically. It revolutionized our understanding of the different levels of character state information on which selection can act, and how. It is the foundation of much of our ability to construct phylogenetic trees. Unfortunately, it has been ignored by the public, by school systems, and very poorly articulated by us to anyone other than fellow academics.
Jason,
When you describe the genetics of living creatures as “sloppy work,” you are making certain assumptions about the purposes and methods of the hypothetical designer. Basically, you are saying “If I were God, I would have done things in such-and-such a way.” When we find that things have not been done that way, you imply that the conclusion is that there is no God. In fact, I believe the correct logical conclusion is that *you* are not God.
Additionally, in Christianity there is the concept of the Fall, which resulted not only in the innate moral depravity of humankind, but in the corruption of the natural world. So it is possible that God made the world in a condition which you would have agreed was perfect, but when the world was corrupted by sin these imperfections were introduced.
I don’t expect a skeptic to find these explanations satisfactory, and better theologians might be able to offer better explanations. But in my opinion, they are enough to demonstrate that science and religion (specifically, Christianity) are not incompatible.
Andrew–
I have read arguments that the panda’s thumb is actually a better design for the peculiar task of stripping leaves from bamboo branches all day than the human opposable thumb. Here’s an article which makes that argument with reference to an article in Nature:
http://www.ideacenter.org/contentmgr/showdetails.php/id/1477
“When you describe the genetics of living creatures as “sloppy work,” you are making certain assumptions about the purposes and methods of the hypothetical designer.”
Does that work both ways then? Can we also eliminate the various arguments offered (not by you) for God based on this or that characteristic of life, its complexity, or even just existence? Does that not also involve assumptions about purposes and methods in the same way?
To respond to something that Josh said above concerning homogeny, what doesn’t creationism predict? It seems to predict heterogeny just as well, if not better.
Spartan,
I don’t see how arguments for the existence of God based on the inference of design in living systems or in the cosmos depend on assumptions about the purposes of the designer. A thing can be designed regardless of the intent of the designer.
But if you can come up with an explanation for how design inferences necessarily assume something about the designer, I’d be interested to hear it.
If an all-knowing, all-wise, all-perfect being chooses to give cats a botched gene for tasting sweetness rather than deleting it entirely, and if I find that to be better explained through evolutionary theory than deliberate design, I guess it only reflects my limited understanding, eh?
And, I can only infer, it’s also a reflection of your own superior wisdom. How perfectly self-serving. Also — how perfectly unfalsifiable. It shouldn’t even count as an argument, let alone an explanation of the phenomenon.
Let me ask you, Eric: We know that sections of genes get deleted. It happens in humans all the time, as well as in every other creature we’ve studied sufficiently to find it. Why is it that deletion is an inadequate explanation for what happened to the cat sweet-tasting gene? Why does it require the hand of God — that is, a miracle — when a perfectly ordinary mechanism is all around us?
Jason,
I think you misunderstand what I am saying here. I am not offering creationism as a better scientific explanation of the characteristics of life on earth. I am simply arguing that modern science is not incompatible with the Bible when both are interpreted correctly.
I agree with you that the apparent deletion in the cat genome which leaves it unable to taste sweetness is not what I would assume one would find based on a belief in a creator God. But in actuality, I do not believe that the Bible states that creation was perfect–even before the Fall. The Bible states that God declared it “good.” (I’m not a Hebrew scholar, but I believe the word used there implies something is suitable for the purpose it was designed for, but does not imply second rate as in good versus great.)
Does a cat suffer because it cannot taste sweetness? It must not be a disadvantage for survival, because if it were this change to the cat’s genome would never have been passed down to the present day.
Three things:
1) Re: the panda’s thumb. I always find it interesting when people cite an ID article that re-interprets a primary scientific article, rather than citing the scientific article itself. I checked the Nature article for myself. It is here: http://www.nature.com/nature/journal/v397/n6717/full/397309a0.html
It concludes that pandas achieve a higher degree of dexterity than was previously thought- but still only what can be expected from opposition of two unarticulated segments. Further, the article points out that the panda’s dexterity system is an exaggerated form of a cluster of parts possessed by all bears- in other words, a structure with homology among bears has become modified in this particular lineage- I note that the ID article conveniently skipped that part. The article specifically does not say that the system works better than an opposed and articulated fifth digit. How could it? There are no panda’s (or closely related species) with actual thumbs against which to perform a functionality test.
Second,
“But if you can come up with an explanation for how design inferences necessarily assume something about the designer, I’d be interested to hear it.”
It’s almost criminal to swing at this softball. Design inferences necessarily assume that there _is_ a designer in the first place. That is an _assumption_, objectively speaking, even if you have faith in that assumption.
This next matter is of critical importance for the rest of this thread. Rigorous attention must be paid to the logic of the selective algorithm:
“Does a cat suffer because it cannot taste sweetness? It must not be a disadvantage for survival, because if it were this change to the cat’s genome would never have been passed down to the present day.”
This is an incorrect interpretation of how selection works. Remember that ‘advantage’ of character states is always relative to two things: variation present within the breeding population, and actual effect on reproductive rate (not survival- longevity experiences far less direct selection pressure than reproductive rate). If failing to taste ’sweet’ had no effect on reproductive success, then it is essentially a neutral mutation, in which case it is neither better or worse- it just is. However (and this is the important part), even if failing to detect ’sweet’ were a disadvantageous state relative to fully functional taste, the sampling error inherent in a finite breeding population can still eventually fix the mutation at 100% frequency through genetic drift (chance). This can happen if sampling error of a breeding population is greater than the value for negative coefficient of selection for the ‘bad’ trait. If that happens, the deletion then cannot be lost from cats because they all have it, and the breeding population is stuck with it. This happens often throughout time, and is referred to as accumulation of ‘mutational load’. It is one of the selective advantages of sexual reproduction, which, through chromosomal recombination, can sometimes concentrate deleterious mutations on single chromosome copies with some probability of purging them from the population- but only if those mutations have not reached 100% frequency among chromosomes carried by the breeding population. Things are not so simple as ‘if it is bad, it will be lost’.
Apologies for the double post- if I want to edit, is there a way to delete a previous version?
Eric,
It seems that design inferences always entail assumptions about the designer, and more specifically his purposes and abilities or lack thereof; if not it seems like that we are stuck with the fact that any imaginable configuration of reality can appear ‘designed’ depending on the hypothesized designer’s qualities and purposes. I inferred, perhaps mistakenly, from your response to Jason that cats can’t taste sweet things perhaps by God’s design, for his own unknowable purpose. At what point do we or can we say, maybe the fact that cats can’t taste sweet things is not ‘designed’ at all? What would we need to know, outside of whether the ‘designer’ exists, to determine that? If we point to the complex interactions of the human body that do appear to be well-designed and induct that we must then have been designed because of how well it all works together, but then turn around and say things like cats’ taste deficiencies or the human appendix are perhaps part of the Fall (again not to ascribe these positions specifically to you), at what point do these bad designs or purposeless designs simply mean they don’t appear to be designed at all? What is the criteria for something to appear not designed?
Spartan,
Thank you for clarifying your argument. I think that while it is possible to conclude with a reasonable degree of certainty that a system was designed, it is much more difficult to be certain that something was not designed.
For instance, if you walk down the street and you see a bicycle in a driveway, you would conclude that the bicycle must have been designed. If you kept walking and saw a twisted piece of metal in another driveway, you might assume it was a piece of junk that was the result of some sort of accident. But it could also be some kind of strange tool that you don’t recognize, or even a piece of abstract art.
Again, the purpose of my comments in this thread is not to argue for the existence of God based on design inferences, but to argue against the notion that an apparently imperfect design refutes the existence of a creator God. I think a more persuasive response to design arguments is to explain how a system that appears to be designed could have arisen from chance.
It’s not simply that the design is “apparently imperfect.” It’s that the genetic blueprints show evidence of being poorly copied.
That’s different, because an apparently imperfect design — imperfect for unfathomable, mysterious reasons — might be explained by an unfathomable, mysterious designer.
But an apparently imperfect design that’s imperfect from a well-understood error — well, that’s another matter. What happened to the cat DNA doesn’t require a creator to be understood at all. It just requires the simple, straightforward understanding that sometimes DNA is copied imperfectly, and that this process is a part of what causes speciation.
So why do we need to invoke the creator here at all? Why not just say that sometimes DNA replication sometimes gets slightly botched and leave it at that?
Andrew,
I went ahead and deleted your duplicate comment. (Unfortunately there’s no way for you, a non-author, to edit or delete comments once posted.)
As for the Panda’s thumb, I agree that it is difficult to say for sure whether or not a human-like opposable thumb would be an advantage over its actual “pseudo-thumb.” As far as I can tell, no one has really attempted to evaluate which design would be better for stripping leaves from bamboo all day, every day. Gould seems to have just assumed the human thumb is better, but I think it is possible that if a human tried to do what a Panda does with its pseudo-thumb for sustained periods of time, he might develop a repetitive stress disorder.
Design inferences necessarily assume that there _is_ a designer in the first place.
No. By “design inference” I mean the logic by which one concludes that there is a designer. I.e., sufficient complexity –> system couldn’t have occurred randomly –> system must have been designed –> there must have been a designer.
As for your explanation of how a harmful trait could reach 100% frequency, you’ve used some jargon that I’m not sure I fully understand. Are you saying that if a certain portion of a population inherited that trait (they survived and reproduced by luck in spite of their genetic disadvantage), and then something killed off the rest of the population (or at least kept them from reproducing), then the population would be “stuck” with that trait? While that makes sense in theory, it seems very unlikely to me that all the individuals without the disadvantageous trait would be wiped out.
But in any case, this is a long way from my main point, which is that systems which seem sub-optimal in some way to a human observer do not disprove the existence of a creator God.
Eric, I’d agree with that for the most part; a key difficulty in this discussion is trying to put our thumb on what ‘design’ even is. Josh seems to have some specific notions about what creationism predicts which is great, but without clarification I have trouble seeing anything imaginable that we can’t say creationism ‘predicts’; certain flavors of Christian creationism certainly predict heterogeny, and Josh feels a common creator predicts homogeny I believe.
I think that puts the cart before the horse; the onus is on the design arguments to be persuasive, a task that won’t be easy when we are admitting that it’s very difficult to explain how we are evaluating design vs non-design. And I’m not sure ‘chance’ explanations are really that persuasive anyway; it seems to be a far more obvious solution to the cats taste deficiencies issue, even though it doesn’t appear to be all that persuasive.
Eric,
Your assertion that a more persuasive response to design arguments would be to explain how a system, with the appearance of design, could have arisen from chance, is exactly right. This is absolutely the most constructive response, but the fact that you are asserting this in 2009, in and of itself, requires a response regarding the intellectual foundation of ID (and I am not attributing that foundation to you- you have just caused it to become topical).
Such explanations (for there have been many that focus on many different organisms or genetic elements) have been documented within the primary literature of evolutionary biology for decades, sharply increasing with the advent of molecular genetics in the 1970s. It isn’t as if descriptions of stochastic processes, resulting in highly adapted character states, have not been published many times over. However, first creationists, and later proponents of ID, have simply ignored all of this while repeatedly asking for “an explanation of how chance can result in something that looks like design.” The very advent of the ID movement, _after_ most molecular evolution had been worked out by the 1990s, simply shows that the people behind the movement don’t even care that the game is already up, or simply weren’t aware. Why would ID proponents do this? I suspect two reasons.
First, the best descriptions of processes in which chance and selection interact are, by definition, intensely mathematical. Read Jerry Coyne and H. Allan Orr’s book ‘Speciation’ to get an idea of this. There are good descriptions of the genetic processes and chance conditions underlying these events, but they are not simple. The best pioneers of evolutionary biology were essentially mathematicians who also liked to observe populations of genetic variants. This makes their work less accessible to the general lay person, but one cannot avoid the fact that formal descriptions of quantitative processes may only be given using mathematical language. This doesn’t make it wrong, for, to the contrary, both molecular and field studies have shown these descriptions to be accurate by using genetic data collected from multiple species. That being said, it is still the intellectual responsibility of ID proponents (or anyone else who wishes to argue the point) to read and digest this body of research before claiming that such explanations have never been given. That would take very hard work (and, frankly, specific graduate level training), and I do not fault anyone for not ‘getting it’ right away. I do, however, fault people for claiming that it has never been done. It has, and at least some of the people at ICR must know this, which makes them rather dishonest in my eyes.
The second reason for not acknowledging the explanations already provided by evolutionary research is this, and this is something that I know is not considered politically ‘polite’, but I honestly think that this aspect of the subject is necessary to address. It is sort of the ‘wiring under the board’. It is simply not in the best interest of ID proponents to acknowledge this because ID is, at its core, a political movement- not a scientific one. It is a body of people who support a theory that they _want_ to be true because they know that if this version of special creation fails, the game is up (never mind that the game was up by 1981 when Li, Gojobori and Nei published their pseudogene paper). They will have to deal with the cognitive dissonance of a profound shift in their reality. Church leadership would have to seriously examine what credibility they have in the eyes of the public. This is a psychological disaster that I suspect many ID proponents want at all costs to avoid. I sincerely feel some sympathy for them, for it cannot last forever, and it will be painful. Those present during that time of realization will have a bed of coals to walk over.
Scientists (or most of us, anyway) don’t have the same problem. My adherence to evolutionary biology, as an explanation of physical reality, is because it has simply been born out by data, provides rules for prediction of some phenomona, and is thus technologically useful. If someone publishes irrefutable evidence that a designer _started_ the process by setting the original primordial cells in motion and then allowed selection and chance to take their course, I wouldn’t care. That wouldn’t change anything about what we know of how things function now, and it wouldn’t change the predictive power of the mathematical theory that has already been worked out. Why? Because the data tell us this: if there is a designer, it chooses never to violate the rules of the evolutionary algorithm. Therefore, such a designer does not have to be part of the predictive model. That doesn’t prove that a designer isn’t there because such a proof is impossible. It does prove, however, that biological evolution must itself have been the chosen technique used for design. I’m fine with that. It happens to be a very effective algorithm for adaptive change.
Spartan,
I agree with you that creationism, for the most part, makes no specific predictions. We could find homologous systems if the creator decided to re-use design aspects in disparate species, or we could find a complete absence of homology if the creator decided to make each species completely unique.
(I have read some very general predictions made by Hugh Ross and colleagues in their old-earth creation model. For instance, they predict that evidence of life should be found very soon after conditions on the early Earth allowed for it, because (IIRC) it would not serve God’s purposes to wait any longer.)
the onus is on the design arguments to be persuasive
Of course it is. I was merely saying that, given a persuasive design argument, the persuasive response is not “Hey, look at this other system over here–why would God have designed it this way?”, but rather an explanation of why the system which does appear to be elegantly designed could have arisen through random changes acted on through natural selection.
Andrew,
If I understand you correctly, you are saying that there are mathematical models which show how complex systems can evolve from the interaction of chance and selection. I am aware of such models, but my understanding is they are abstract. To my understanding, most ID proponents do not argue that it is impossible for any complex system to evolve by chance acted on by selection. Instead, they argue that there are particular systems in biology which are “irreducibly complex.” Does the work you have mentioned address these specific systems?
Jason:
So why do we need to invoke the creator here at all?
I’m not saying we do need to invoke the creator. I think evolution is a good model. I simply disagree with trying to use findings from science as proofs against the existence of God. I think it’s just as wrongheaded and unproductive as insisting that if science doesn’t line up with one’s particular interpretation of scripture, then the science must be wrong.
Evolutionary theory certainly isn’t a disproof of God, but it does knock out an entire line of proof of God, the one that argued that only the Creator could be the originator of the various species, and of their harmonious, rationally designed working parts.
Of course, this line of proof is really just a pale shadow of the proof from the fact that there is something rather than nothing. But… it’s nearly anyone’s guess at this point what specific type of Creator this proof implies.
Eric-
>No. By “design inference” I mean the logic by which one >concludes that there is a designer. I.e., sufficient >complexity –> system couldn’t have occurred randomly –> >system must have been designed –> there must have been a >designer.
But then yes, the designer is an assumption. It is assumed that there is a level of complexity that the evolutionary algorithm could not produce. What this level is has never been quantified, by definition, because such a system has not yet been found on earth. This is related to what you say below, so I’ll move on to that.
>If I understand you correctly, you are saying that there >are mathematical models which show how complex systems can >evolve from the interaction of chance and selection. I am >aware of such models, but my understanding is they are >abstract. To my understanding, most ID proponents do not >argue that it is impossible for any complex system to >evolve by chance acted on by selection. Instead, they >argue that there are particular systems in biology which >are “irreducibly complex.” Does the work you have >mentioned address these specific systems?
I am not referring to the abstract complexity models. Those are attempts at general models for explaining complexity per se. I am referring specifically to three things: 1) models of population genetics that cover everything from highly complex mating systems to the arms race between parasites and their hosts; 2) the formal theory that predicts patterns of DNA sequence change over long periods of time, and the subsequent collection of DNA sequence data from living species that validated this body of theory; 3) The accumulation of genome complexity that arises from accidental duplication events in which genes, whole chromosomes, or even whole chromosome sets are duplicated. The last provides extra genetic material that can result in novel function when those extra copies accumulate mutations that change what they originally did. The best example that I know are the crystalline proteins of the vertebrate eye lens. They are coded for by a gene that was once a duplicate copy of one of the ancient metabolic enzymes. For #2, the most important insight was made by Motoo Kimura in the 1970s when he published the neutral theory of molecular evolution. More on that later- there is a large collection of papers that I just handed to Chuck, and I will allow him to have a crack at it before I say any more. I don’t want to steal his fun.
The systems to which you refer as being irreducibly complex were labeled so by people who simply did not know how to reduce them. That is an experimental or scholarly limitation, not evidence of a designer. To argue that they were designed, and, hence, created specifically for those purposes, overlooks the fact that those systems frequently use parts that are derived from older structures. I recommend delving into literature on evolution of the vertebrate eye, as mentioned above, for this purpose. Or evolution of ribosomes, for that matter.
On the lines of what Jason is saying, as a concluding remark let me just point out that even as strong an atheist as Richard Dawkins has said that evolutionary biology does not disprove the existence of God. Nothing can. But evolutionary theory does provide a natural explanation for the unity and diversity of living forms seen on Earth that does not rely on supernatural forces. Evolutionary theory does allow atheism to be intellectually coherent for this reason, but it certainly doesn’t disprove the existence of supernatural forces. The question of the interface between supernatural forces and natural ones is one that has always bothered me, though. At some point, a ghost must have an effect on matter – but on a mechanical level how is this accomplished? This question applies not only to creation by a supernatural force, but to the theory of mind and soul of the ghost in the machine, too.
But I’ll have more to say on this in later posts.
Jason/Chuck,
Fair enough on evolution being a persuasive response against the argument that only God could have created the diversity and complexity of life on earth.
I’ve never been a big fan of the type of argument which says “You can’t explain this particular phenomenon with science, so therefore God must exist.” That only seems persuasive until someone comes up with a reasonable model to explain the phenomenon through natural means. (And man’s ability to come up with rational hypotheses to explain phenomena appears to be limitless.)
I would also add from a theological point of view, if there were incontrovertible evidence of the existence of God that not even the most intelligent humans could escape, that would make faith meaningless. It is impossible to argue someone into belief against their will. Instead, the proper role of apologetics is to remove obstacles from someone who is willing to believe but has questions, and to strengthen and edify believers.
Oh, I forgot to add–thanks for the interesting discussion. It’s nice to be able to delve into topics without people yelling at each other.