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Theistic Evolution: Common Descent or Common Designer?

Posted By Randall D. Isaac, Thursday, April 5, 2018

The second major scientific critique of theistic evolution in this book claims that universal common ancestry, or simply, common descent, is not supported by the evidence. Common descent is the startling hypothesis presented by Charles Darwin (and Alfred Russel Wallace) in 1859, suggesting that all life forms have descended from “…a few forms or one…” At that time, there was scant evidence to support such an audacious claim. In the next half-century, most of the data obtained seemed to point against it. Lord Kelvin noted from thermodynamics that the earth was perhaps no more than 25 million years old, ensuring that there was not enough time for all life to evolve from the same source. The fossils that were discovered during that time could not be dated with any reasonable accuracy, leaving a puzzling set of data.

At the turn of the century the tide began to change. The discovery of radioactivity opened the door to solving both major dilemmas. It provided the source of heat that Lord Kelvin needed to realize that the earth was indeed very old, in the billions of years. Radioactivity was also the key to determining the age of the fossils. Amazingly, the story told by the fossils fit dramatically into Darwin’s proposal. In addition, the rediscovery of Mendelian genetics gave credence to the crucial role of inherited traits. In another half-century, the discovery of DNA added a major corroboration to Darwin’s theory. In yet another half-century, the ability to sequence genomes provided the icing on the cake, permitting extraordinarily detailed confirmation of common ancestry. There could be no further doubt.

Or could there be? The authors of this book present two arguments that they believe nullify the firm conviction of nearly all biologists. They are so confident in the strength of their arguments that they claim evolution is not even sufficiently viable for anyone to consider integrating it with Christianity. The two arguments are

1.       There are observations that cannot be explained by common descent

2.       The alternative explanation of common design is a superior claim

I will discuss only two of the types of observations they present as being contradictory to common descent. The first is the inconsistent pattern of hybridization found in nature. They list page after page of details of families and genera in which some species hybridize and others don’t. Their point is simply that if common descent were true, then all species within a family or genus would either all hybridize or all not-hybridize. What they fail to recognize is that the ability for species to hybridize depends on more variables than the proximity of their common ancestor. Both environmental factors and the specific types of differences underlying their differentiation have a great bearing on the ability to hybridize. In other words, while it is true that a near common ancestor would increase the likelihood of the ability for two species to hybridize, other factors come into play that prevent these observations from nullifying common descent.

The second type of observation they present is the occasional lack of orthologous genes. Orthologous genes encode for the same function in different species and are almost identical. Consistent with common descent, there are only a few differences in the genetic sequence of these orthologous genes due to a slightly different history of mutations. I recall hearing Paul Nelson’s talk at the ASA 2012 meeting at Pt Loma, CA. He described genes in certain species that had no orthologous gene in an ancestral or closely-related species. His point was that if common descent were true, all genes should have orthologous forms in closely-related species. The frequency of these “orphan” genes without an orthologous gene in closely related species, however, was very low, less than 1%. I later learned from my biologist friends that even today’s highly sophisticated sequencing technology can only detect with ease about 90% of an arbitrary genome of a species. The remaining 10% or so are extremely difficult to find and are generally not worth the trouble or the cost. A missing gene in a species could well be part of the remaining 10%. Consequently, an inability to identify a small number of orthologous genes in closely-related species is not a fatal contradiction of common descent.

Other types of examples are offered but, like these two, are the result of a misinterpretation of the scientific data. Many of the issues relate to familiar claims of missing links, sudden appearance of species, rapid extinctions, or a too rapid pace of evolution. Not one of these issues represents a fundamental contradiction of evolution but rather is within the range of complexities being explored within the realm of evolution.

The second main argument presented in the book is that common design is an alternative and superior explanation for all the observations. Simply put, the theory of common design says that any similarity between species is the result of a common designer who uses a common building block to design various species. Any differences between those species is the result of that common designer recognizing the different functional needs that those species may have. Voila, all observations have been explained. Similarly, the large number of pseudogenes are predicted to have some residual value for their organism, thus explaining their existence by a yet-to-be discovered functionality. For example, the defective gene for vitamin C in primates is imagined to have some unknown function, presumably more necessary than making vitamin C.

In a later post we will explore one of the philosophical problems associated with the assertion of a common designer. Here we comment on the scientific description itself. First of all, the common designer concept is not falsifiable. A similarity and a difference between two organisms are equally “explained” by the proposed existence of a common designer, which has not been observed. No evidence could render the explanation to be false. Secondly, the hypothesis provides no basis for understanding under what conditions there are similarities and when there might be differences. The only vague rationalization is that the alleged “common designer” knew it was better to have a similarity or a difference. Finally, the assertion of a common designer is best called “creation with the appearance of common descent.” Like the concept of “creation with the appearance of age” in the young-earth claims, it cannot be scientifically or logically disproved definitively but is neither theologically nor pragmatically defensible.

Tags:  theistic evolution 

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Tony Isaac says...
Posted Tuesday, April 10, 2018
As with "creation with the appearance of age," I reject "creation with the appearance of common descent." With that said, it makes sense that the various creations by a common creator might appear to have common descent, as a side effect of having a common creator. This is not he same as creating life in such a way as to make it "deceptively" look like common descent.

As a software engineer, I can look at software and tell you 1) how skilled the creator was, 2) how intelligent the creator was, 3) how much effort was put into the design by the creator, 4) the elements of design that the creator considered important, and many other attributes of the creator. I can do this because I thoroughly understand HOW (the process by which) software (or anything) is designed and developed.

When I look at the design of life through the eyes of an engineer, I see a highly skilled, highly intelligent Creator, one who spent much effort working out the many design choices and tradeoffs, to produce thriving life forms. If indeed random chance produced all of life, then that random chance produced a creation "with the appearance of a designer."

I accept that life evolves, but I can't accept that life could have designed itself spontaneously. Perhaps that is why I'm an engineer rather than a scientist!
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David E. Singer says...
Posted Wednesday, April 11, 2018
Tony, I share your propensity to see an astute designer as I marvel at God's creation. I think this perspective is in keeping with revelation. But then I too am not a scientist nor even an engineer. I do try to fathom, as best I can, the latest scientific explanations and discoveries. I've read "The Language of God" by Francis Collins and found it convincing. Science, by definition, searches for a sequence of "natural" causes. As Randy points out, the 'common designer' concept is not falsifiable. From my perspective no miracle, by definition, is (they aren't repeatable) Falsifiability is required to pass as good science. But in the end we know that God created all that exists. But like miracles in general, we don't know how. That remains the purview of science. So, when I look at evolution as a closed system of explanation, I say there's still that missing ingredient of the Divine. I can marvel at the result without knowing exactly how it all came about but also knowing it wasn't just by accident or a consequence of random probabilities.

There's this tendency to cast revelation against science when both are needed for a fuller understanding. Revelation points to the who and why; science elucidates the how. Neither is sufficient alone. I find it interesting that, as much as we know of life, its complexity and origins still baffle and astound us.
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Randall D. Isaac says...
Posted Sunday, April 15, 2018
Tony, I appreciate your comment and the opportunity to clarify some of the key issues. First, I should point out that I think the title of my post is somewhat misleading. By saying “Common Descent or Common Designer” I erroneously give the impression that these are mutually exclusive. They aren’t. As Christians, we all believe that God created everything and that he is the common creator/designer of all life and all matter. The issue is how God created life and whether or not he used evolution as the means of creation. Perhaps the title should more appropriately have been “Common Descent or not” implying that the question is whether or not God used a method other than evolutionary common descent to carry out his creative intent.
On one level, the analogy you offer of an engineering design or a computer program seems relevant but I would suggest that a different analogy would be closer more accurate. We all have a lot of experience with human design activity but what is our experience with biological design activity? We have no experience at all of any intelligent being creating any synthetic life, notwithstanding all the incredible progress on biotechnology today. Rather, our ubiquitous experience is that of observing biological reproduction with variation. We observe it in every species in the world. We know much, though we still have more to learn, about the types and rates of changes that occur in both the genetic and the epigenetic composition of life. The overwhelming evidence of the vast majority of genes is that the similarities and differences between genes of related species are consistent with this pattern of reproduction having continued ever since the origin of life.
Why then is there such a compulsion to reject common descent and to insist that our creator used a different method? Indeed, no alternative method has yet been offered other than to speculate on a sudden appearance of a new species. Or perhaps reproduction with divine variation instead of natural variation. No evidence that I am aware of has ever been offered for an alternative path. Instead, the argument appears to be that common descent doesn’t explain all the data. This suffers from the problem that Robert Bishop highlighted in his December 12, 2017 comment on this blog. His analysis would also apply to this situation: “There are at least two problems with this response. First, it's a reasoning fallacy known as unobtainable perfection: Increase the evidential demands beyond what can reasonably be met; proclaim victory when the demands cannot be met. Second, the demand would prove too much. We have relatively few explanations in the sciences that have every detailed step filled in. The implication is that there few acceptable explanations in any of the sciences. A conclusion that serves as a reductio of the demand.”
In other words, while there are many situations that are not yet understood, these do not constitute refutation of common descent. The point I was trying to make in my post is that no evidence has yet been offered that conceivably falsifies common descent. Some examples of hybridization, orphan genes, remarkably rapid development, etc., may not be fully explained but not a single one has been shown to contradict the possibility of common descent. Meanwhile, the existence of a common designer is not a denial of common descent nor is it an alternative explanation.
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Randall D. Isaac says...
Posted Sunday, May 6, 2018
Tony, I’d like to comment further on your remark that “I can do this because I thoroughly understand HOW (the process by which) software (or anything) is designed and developed.” I think you have an excellent point, one which strengthens the argument for an evolutionary design of all life. The key is to thoroughly understand how the design is done. We humans are very creative and enjoy designing and building all types of machines and pieces of art. We are accustomed to thinking that, by analogy, everything must go through a similar process. As an all analogies, we must understand the differences as well as the similarities. So we need to understand thoroughly just HOW any organism of life comes into being.
We must note that in no case whatsoever is an organism assembled from pre-existing components. There is no warehouse inventory of parts, like hearts, lungs, skin, bones, etc. that are assembled into a functional individual. Nor is there a reservoir of each cell type from which the body is composed. In every case, an organism develops through growth from a single initial zygote, as incredulous as it may seem. Going even deeper into the biochemistry, we learn how this zygote grows and is differentiated into all the necessary cell types. In no case is an external agent involved except as the instrument by which two gametes unite to form the zygote. Those gametes are, in turn, generated through biochemical processes from each parent with no access by any external agent. The process differs markedly from that in any software or any hardware that has ever been created by an intelligent being.
So as you astutely point out, thoroughly understanding the process by which any living organism is designed and developed is critical to understanding the origin. All of our experience, without exception, is that every individual organism develops from its initial zygote, with an inherent variation due both to internal processes of gamete formation and to external mutation-inducing events and due to the influence of the microbiome as well as responses to the environment. Even with modern biotechnology, there has been no ab initio creation of even the simplest form of life by an intelligent agent. We know of no other process. And the one we know is precisely the evolutionary process. (Again, this does not refer to the origin of life for which there is yet no scientific theory but only refers to the origin of species from an initial form.)
For many, there is simply an argument from incredulity. You described that argument well when you said “I accept that life evolves, but I can't accept that life could have designed itself spontaneously.” However, you left ambiguity about whether you accepted universal common descent but not abiogenesis or whether by “designed itself” you meant the design of all species by universal common descent. But it seems that almost everything in modern science could be defeated by an argument from incredulity. Much in relativity and quantum physics makes no common sense. Just so, in biology we must look at the evidence and all evidence uncovered so far points to universal common descent.
Just what is that evidence? To cite a few: universal building blocks of nucleosomes; universal building blocks of amino acids; universal usage of the same genetic code, except for a couple dozen minor variations for mitochondria, for example; high degree of similarity in genes, gene placement (senteny), chromosomes, etc. that scale with relationships; traceable descent of specific mutations and unique genetic segments; lack of any fundamental differentiation between body types; etc. To date there has not been a single credible report of data that would falsify universal common descent. All rational arguments of dissent are in situations that are not fully understood but do not qualify for falsification.
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Tony Isaac says...
Posted Saturday, May 12, 2018
One statement you made isn't quite correct, and is crucial. "The process differs markedly from that in any software or any hardware that has ever been created by an intelligent being."

Actually, there has been much research and success in recent years in the development of self-assembling nanomaterials. These structures have grown quite complex and sophisticated, and exhibit properties such as self-healing and responding to various electrical or chemical stimuli. Many can even "reproduce" under appropriate conditions. It's not inconceivable that such structures will eventually "evolve" to the point that they mimic significant components of what we now call "life."

The design of such self-assembling materials requires significant investment of time, money, and expertise, and much trial and error. These nanomaterials certainly don't spring into existence by random chance!

When I speak of the engineering behind life, I'm talking about the engineering of molecules such as DNA, the highly complex process by which mitosis occurs, and so on. I'm not at all imagining a Creator hunting for parts from some bio-warehouse. Rather, I imagine a Creator who engineers nanomaterials that, through a highly-choreographed process we call mitosis, are able to reproduce and live and breathe.
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Randall D. Isaac says...
Posted Monday, May 21, 2018
Tony,
I am a bit confused about where you and I agree and where we disagree. It seems as if we are in general agreement but your phrasing suggests some differences. I think we have two areas of agreement and two where we may disagree. Perhaps you could clarify?
1. We agree that there is a remarkable degree of similarity between both the structure and the process of information in an engineering design/software program and a biological organism.
2. Do you disagree with my view that there are also some profound differences? Some of the most significant are that biological organisms change through internal processes without an external agent while engineering/computer systems don’t. More to the point, engineering and computer systems inherently involve symbolic and abstract relationships which require external intelligent agents while biological systems have no such symbolism.
3. We agree that we all have a common Creator and that God created all things.
4. Do you disagree with the view of universal common descent?
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Terry M. Gray says...
Posted Tuesday, July 3, 2018
"Or" ?
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Randall D. Isaac says...
Posted Tuesday, July 3, 2018
Agreed, the « or » is wrong in that headline Should be « and » or as I said in my first comment, «  I should point out that I think the title of my post is somewhat misleading. By saying “Common Descent or Common Designer” I erroneously give the impression that these are mutually exclusive. They aren’t. As Christians, we all believe that God created everything and that he is the common creator/designer of all life and all matter. The issue is how God created life and whether or not he used evolution as the means of creation. Perhaps the title should more appropriately have been “Common Descent or not” implying that the question is whether or not God used a method other than evolutionary common descent to carry out his creative intent.« 
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Peter Karlskov-Mortensen says...
Posted Saturday, July 28, 2018
Even though I agree on the general lines in your post I have to add a comment on your comments to the 'second main argument'. It appears that the "yet-to-be discovered functionality" of pseudogenes is already being discovered. The ENCODE project has shown that almost all of the human genome is expressed - including the pseudogenes, and recent research has shown that pseudogene transcripts can regulate expression of the parental gene - see for example https://onlinelibrary.wiley.com/doi/abs/10.1111/jcmm.12952. A lot of research has been done on the function of pseudogenes in cancer.
With the comments to this post in mind, let's appreciate how much we agree. We have a great God who created a truly marvellous world. Yes, he did use the same building blocks over and over again, and yes he did do it very systematically. Life and world is a miracle! As a scientist I just have the humble hope that I might be able to figure out a little bit about how he did this miracle.
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Peter Karlskov-Mortensen says...
Posted Saturday, July 28, 2018
...and another comment to the hiding orthologous genes:
The 10 percent of the genome which is hard to sequence is primarily the highly condensed centromeric and telomeric regions (highly repetitive regions) and regions with high GC content. Protein coding genes are normally not difficult so sequence (except exon 1 which is often in a high GC region). There are a number of theories explaining the existence of orphan genes (for a quick overview just see Wikipedia). I have one theory which I haven’t seen anywhere yet: For many gene functions there is a great deal of redundancy in the genome. For example, we all have a significant number of deleterious mutations in protein coding genes and still we work just fine. Imagine a simple example with a specific cell function for which gene A is primarily responsible, but another (inferior) gene B can take over “in case of emergency”. A deleterious mutation in gene A in a specific species S will put gene B under strong evolutionary constraint and preserve it in future generations. In all other species with an intact gene A, the inferior gene B may deteriorate due to random mutations. The B gene survives only in species S. But it is too easy to sling out hypotheses like this and we all fall into a mess if the discussion runs out on such tracks. However, maybe my theory isn't new at all. If anyone in this forum could add anything to it I'll appreciate it.
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Randall D. Isaac says...
Posted Sunday, August 5, 2018
Peter,
Thank you very much for your comments and I appreciate the opportunity to make corrections and clarifications. I did not mean that pseudogenes could not have a function for the argument to hold. It is clear the pseudogenes once had the function of generating particular proteins but now due to a mutation of some kind can no longer do so. The disabled gene for vitamin C in primates is a great example. Any alternative use for which this pseudogene might have adapted does not negate that change. Tracking the specific disabling mutations shows rather clearly the hereditary path. My overall point is that pseudogenes are a very useful marker to help trace common ancestry. Alternative uses may well exist with no impact to the argument for that ancestry. The claim that an alternative function of a pseudogene means that an intelligent designer chose or needed to use that structure to carry out that function, does not follow from the observation. Cells are far more resilient than that.

Incidentally, the ENCODE project was very interesting and has been used for many claims, not all of which are sustained under scrutiny. I think we need to keep in mind that the ENCODE team used a rather unique definition of function, citing at least five different definitions that they included. One of them was simply transcription into RNA fragments but without verification of whether these segments played a significant role in the life cycle of that cell. It also should be noted that even with the broadest definitions of function, the ENCODE team was still left with a rather sizable fraction of the genome that had no function even in their definition, ranging widely on the order of 20% or more. In my opinion, neither the discovery of a function for DNA that was thought to be useless nor the existence of DNA for which no function exists is supporting evidence for either evolution or intelligent design. We are all interested to learn more about the fascinating functions of DNA, wherever that exists.

As for orphan genes, thank you for the additional helpful information. Again, I did not mean to imply that these orphan genes were solely due to the inability to find some percentage genes. I intended to say this is one of several reasons that may account for the existence of orphan genes. There are many other reasons like the one you helpfully offered. My intent was to show that the existence of orphan genes does not negate the possibility of evolution.
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