Intelligent Design Discussion

[one.opinion]

"Intelligent Design" (or ID) is a common term as Christians discuss the complexity of life we see today. I share a lot of common sentiment with the supporters of ID. First, most of them are genuine Christ-followers like I am, and believe that all creation is due to His will and for His pleasure. We (ID supporters and I) also believe that the universe and living things we can observe today are better explained by a Creator and His actions through naturalistic processes He set into place than in naturalistic processes operating on their own.

The Discovery Institute (the most prominent organization devoted to the study and promotion of ID) defines Intelligent Design as this:

Quote

The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

There is one thing I like and a few things I dislike about this definition. First, I 100% agree that the features of the universe and of living things are best explained by an intelligent cause. Now on to some of the things I disagree with.

* I understand it is for political reasons, but I do like to state that the "intelligent cause" is Jesus Christ, my Savior and Lord, rather than leave that "cause" so vague.

* I also object a bit to the use of "theory" in this context. In scientific terms, a theory must be testable and supported by positive evidence. Bio-Complexity, a scientific journal occasionally published by the DI (Discovery Institute - I know... too many "D"s and "I"s...) does not publish any research that supports an "intelligent cause", but merely publishes results that argue against naturalistic evolution. This does not qualify ID as any sort of theory by standard scientific use of the term.

* The focus of this definition starts with "features of the universe and living things", but abruptly shifts to focus solely on natural selection. There seems to be a bit of an obsession with taking down "Darwinian natural selection", as if the scientific understanding of evolution has not advanced in the last 150 years. Among the prominent ID figures, like Michael Behe and Stephen Meyer, there seems to be much less interest in the "universe" than there is for the inadequacies of "natural selection".

Overall, I find myself sympathetic to ID in concept. For example, I find it more plausible to accept God's direct creation of the first living cells than than to accept random chemical evolution that eventually developed into living organisms. However, I disagree with how ID is actually presented, such as the focus on arguing against "natural selection" and what I perceive as the lack of engagement with recent scientific findings.

@Starman @The Barbarian, what are your thoughts?

[Starman]

First of all, I need to apologize in advance since I won't be able to engage on this topic at your level. This is a complex subject and my knowledge is cursory at best (which you will soon see by my comments on the subject). I'll probably be asking more questions than giving answers.

With that said, I agree that ID falls short with respect to testability and predictive power. Meyer gives the example of ID making the prediction about "junk DNA" actually being essential for gene regulation, which apparently is now being confirmed by experiment.  Another example is the claim by evolutionary science that common descent is confirmed by "broken" genes showing up in multiple related species, since it's unlikely that the same defects arose independently.  Apparently some 0f these genes are actually fully functional, which may dampen the evidence for common descent.  I assume that evolutionists also have good arguments against these claims.

Regarding ID's focus on refuting natural selection, it seems to me this is warranted since natural selection is the lynch pin of evolutionary theory, without which it falls part (correct me if I'm wrong).  If natural selection lacks the creative power to explain macroevolution then another TBD process must be invoked.  According to Meyer evolutionists have already come to this conclusion and other theories are being posited.  The need for new explanations would seem to point to the inherent weakness of the darwinian paradigm.

Regardless, IMO the weaknesses of ID does not take away from the fact that it provides a better explanation of complexity biological life than the standard Darwinian model (evolutionary theory has "evolved" much over the last few decades and I can't speak to the latest assumptions).  This is true particularly given the problem of vast amounts of biological information being infused into the genome over short time frames (e.g., the cambrian explosion), the low probability of beneficial genetic mutations,  and the irreducible complexity problem (some biological structures have no functional precursors which would be required by a Darwinian process).  

Question: Do you accept standard evolutionary theory as currently taught in academia? If so how do you address the kind of challenges that come from Meyer etc.?

Edited February 25, 2020 by Starman

[The Barbarian]

8 hours ago, Starman said:

With that said, I agree that ID falls short with respect to testability and predictive power. Meyer gives the example of ID making the prediction about "junk DNA" actually being essential for gene regulation, which apparently is now being confirmed by experiment.

Since this was actually suspected in the late 1960s,  and confirmed in the 1970s, and ID was invented in the 80s, it shows ID's "postdictive" power, predicting things science has already discovered.

 

Journal of Molecular Biology

Volume 107, Issue 4, 15 November 1976, Pages 491-525

Sequence analysis of the 3′ non-coding regions of rabbit α- and β-globin messenger RNA

The significance of this homologous sequence is unknown but it may be a signal for termination of transcription or a recognation site for some regulatory protein common to these and possibly all eukaryotic mRNAs. Second, these studies have indicated that the 3′ non-coding sequences of these two mRNAs may be longer than the corresponding 5′ non-coding sequences. In particular, the rabbit α-globin mRNA sequence contains a region that may be related to human “constant spring” α-globin (Clegg et al., 1971), so that the 3′ non-coding region of this mRNA is approximately defined as 100 nucleotides, whilst the 5′ non-coding region is about 50 nucleotides. The greater length of the 3′ as compared with the 5′ non-coding region of these mRNAs may be a common feature of many eukaryotic mRNAs.

 

Nucleic Acids Res.

1979 Jun 25;6(8):2647-65.

Characterization of in vitro transcription initiation and termination sites in Col E1 DNA.

Patient RK.

Abstract

Overlapping restriction fragments from the region between the single Eco R1 site and the origin of replication of the plasmid, Col E1, have been utilised as templates in an in vitro transcription assay using E. coli RNA polymerase. Transcription towards the single Eco R1 site is initiated at a point 415 bp to the origin side of that site. In vivo, transcription starting at this point probably produces the mRNA for the colicin immunity protein. Transcription away from the Eco R1 site is initiated at a point 140 bp to the origin side of that site and terminated 30 bp further on. This terminator is probably the point at which transcription of the colicin gene is terminated in vivo. DNA sequence analysis in both these regions demonstrated several similarities to other prokaryotic regulatory regions. 50% homology between the putative immunity promoter and other prokaryotic promoters is apparent, so are similarities in AT-content. Upstream of the ATG start codon the sequence PuPuTTTPuPu and a termination codon (TAA) appear; both are typical of prokaryotic ribosome binding sites. The colicin terminator demonstrated similarities to other rho-independent prokaryotic terminators: a GC-rich region with termination in an adjacent AT-rich region containing T clusters on the non-coding strand. The possible role of initiation upstream from the colicin terminator is discussed.

[The Barbarian]

9 hours ago, Starman said:

Another example is the claim by evolutionary science that common descent is confirmed by "broken" genes showing up in multiple related species, since it's unlikely that the same defects arose independently.  Apparently some 0f these genes are actually fully functional, which may dampen the evidence for common descent.  I assume that evolutionists also have good arguments against these claims.

This would still indicate common descent, since even if the mutation didn't break the function of the gene, the likelihood of two organisms getting the same mutation by chance is so small as to be negligible.

9 hours ago, Starman said:

Regarding ID's focus on refuting natural selection, it seems to me this is warranted since natural selection is the lynch pin of evolutionary theory, without which it falls part (correct me if I'm wrong). 

Since natural selection has been demonstrated to produce increases in fitness and even a new structure in organisms, that's not an arguable issue.

9 hours ago, Starman said:

According to Meyer evolutionists have already come to this conclusion and other theories are being posited.  The need for new explanations would seem to point to the inherent weakness of the darwinian paradigm.

Meyer's confusion is in supposing that Darwinian theory only allows evolution under natural selection.   That's not the case, and there is solid theoretical and observational support for that theory.   Motoo Kimura's neutralist work, for example.

His other misconception is to suppose that it's this mechanism, or that mechanism, or something else, in isolation.   That's not what we see:

Natural Selection, Genetic Drift, and Gene Flow Do Not Act in Isolation in Natural Populations

By: Christine A. Andrews (Biological Sciences Collegiate Division, University of Chicago) © 2010 Nature Education 

 

In natural populations, the mechanisms of evolution do not act in isolation. This is crucially important to conservation geneticists, who grapple with the implications of these evolutionary processes as they design reserves and model the population dynamics of threatened species in fragmented habitats.

 

9 hours ago, Starman said:

Regardless, IMO the weaknesses of ID does not take away from the fact that it provides a better explanation of complexity biological life than the standard Darwinian model (evolutionary theory has "evolved" much over the last few decades and I can't speak to the latest assumptions). 

That is the latest ID assumption.    ID has taken a beating over the past few years, as its religious basis was made clear in the Dover trial (where IDer Michael Behe admitted under oath that ID is science in the same sense that Astrology is science), and then as repeated observations have shown Darwinian processes to function as predicted to increase fitness, produce new species, and to change fitness phenotypes.   Would you like some examples?

 

9 hours ago, Starman said:

This is true particularly given the problem of vast amounts of biological information being infused into the genome over short time frames (e.g., the cambrian explosion),

That assumption was invalidated when it became clear that complex multicellular animals had evolved long before the Cambrian.   Some of the body plans of Precambrian animals  are clear precursors to later, Cambrian animals.   At one time, IDers took some comfort in supposing that the Precambrian biota were not animals; that fell apart when cholesterol molecules were isolated from some of them.

And "information" is not what IDers seem to think it is.   Any new mutation in a population will increase information.   Would you like to see a very simple example of how it works?

 

9 hours ago, Starman said:

the low probability of beneficial genetic mutations

 Show me your numbers.    Then we'll take a look and see if it fits the rates of evolution we observe.

9 hours ago, Starman said:

and the irreducible complexity problem (some biological structures have no functional precursors which would be required by a Darwinian process).  

Show us one.    There are some reasons why Behe now admits irreducible complexity can evolve.   One is a directly observed case of it happening.  Would you like to see that?

 

9 hours ago, Starman said:

Question: Do you accept standard evolutionary theory as currently taught in academia? 

Would you outline the major points of "standard evolutionary theory" as you suppose it's currently taught in academia?    Given the different opinions on things like drift, kinship selection, and the like, which of those do you think is the "standard?"

If you mean the basic points of Darwinian theory, plus genetics, then yes, those are as solid as ever, with more and more observational evidence supporting them.

9 hours ago, Starman said:

If so how do you address the kind of challenges that come from Meyer etc.?

Mostly the way we've just pointed out the flaws in his thinking.   Stuff like that.

 

 

 

 

.

 

Edited February 26, 2020 by The Barbarian

[Starman]

Barbarian:

Thanks for the input.  However, as you already knew my knowledge of the subject is insufficient to have an intelligent conversation with you (I’ve studied enough to be a little dangerous, but not enough to argue the fine points).  I assume there are smart people who can challenge your assertions but I’m not one of them.  Hope you can find someone to play ball on your field, as playing alone isn’t fun.  
 

[one.opinion]

Alright, so I'm guessing that @The Barbarian is not a big fan of Intelligent Design :-P

On 2/25/2020 at 10:50 AM, Starman said:

First of all, I need to apologize in advance since I won't be able to engage on this topic at your level.

Absolutely nothing to apologize for in that. Not everyone has the rare combination of interest and opportunity for advanced-level studies. However, we can always learn little bits here and there. I learn new things about biology on something close to a daily basis (not so much on Saturdays and Sundays!).

On 2/25/2020 at 10:50 AM, Starman said:

Meyer gives the example of ID making the prediction about "junk DNA" actually being essential for gene regulation, which apparently is now being confirmed by experiment.

A large portion of "junk DNA" is in the form of 3 different types of retrotransposons - LTR transposons, SINEs and LINEs. These retrotransposons make up abour 44% of the entire human genome, which is a staggering number when considering that the portion of the genome comprised of protein-coding exons is only 1.5%. There is considerable evidence (based on leftover signatures of now-broken genes) that a large portion of these retrotransposons originated from infection by retroviruses over the history of the hominid genome. Another large portion of that "junk DNA" is from gene introns, that are rather limited in function. There are many examples in the literature of certain retrotransposon and intron sequences that have been confirmed to have particular functions, but the overall theme remains the same. These sequences are not particularly conserved, so their role in cell activity appears to be more accidental than a requirement. This is not surprising when considering the biochemistry of molecules in the cell - these biomolecules are chemically-driven to interact.

Barbarian also makes a good point that there is a bit of revisionist history in ID camps that "we are the only people that predicted function in non-coding DNA!" when it really isn't the case.

On 2/25/2020 at 10:50 AM, Starman said:

Another example is the claim by evolutionary science that common descent is confirmed by "broken" genes showing up in multiple related species, since it's unlikely that the same defects arose independently.

Yes, genomes are littered with pseudogenes that are products of duplication and divergence. Duplication and divergence occurs when a DNA region containing a gene becomes duplicated, including adjacent regulatory sequences. With two copies of a functional gene intact, the constraints of conservation are reduced and more mutations can accumulate in both genes, if at least one of the two retains function. These accumulated mutations result in sequence divergence which can also result in functional divergence. We can look at sequences of hemoglobin, for example and see DNA similarities between different (but related) genes that are expressed in the embryo, fetus, and after birth. The alpha and beta globin clusters also have neighboring pseudogenes that result from sequence divergence resulting in non-functioning genes. Sometimes the divergence allows the formation of a gene that codes for a gene product with slightly different function, and sometimes the divergence breaks a functioning gene into a non-functioning one. Rarely, a pseudogene is observed without any paralog sequences showing where it came from. The GULO pseudogene is a good example. While many mammals (including some primates) can make vitamin C, most primates cannot. However, there is a broken version of the GULO gene present that is still easily identifiable due to the sequence similarity to the functional gene. I'd have to look at the examples of "functional pseudogenes" to comment any further.

Sorry, it is getting later in the afternoon than I intended, so I am jumping to the end of the post. (I might go back and address more later).

On 2/25/2020 at 10:50 AM, Starman said:

Question: Do you accept standard evolutionary theory as currently taught in academia? If so how do you address the kind of challenges that come from Meyer etc.?

As an academic myself, I do teach the scientific evidence supporting evolution. I also tell my students about how my Christian faith relates to how I see the scientific evidence. Personally, I see incredible power, mind-blowing intelligence, delicate beauty, and a Creator so intimately involved with His creation that He cares about every single organism in it. When I was a YEC many years ago, creation filled me with wonder, but when I see a Creator that worked through such an amazing process, my appreciation for His surpassing attributes reach an entirely new level.

More about challenges to come...

[The Barbarian]

20 hours ago, Starman said:

Thanks for the input.  However, as you already knew my knowledge of the subject is insufficient to have an intelligent conversation with you (I’ve studied enough to be a little dangerous, but not enough to argue the fine points).  I assume there are smart people who can challenge your assertions but I’m not one of them.

It's not rocket science.   If you care about it, you can learn.   I once knew a body repairman who had a pretty good grasp of evolutionary theory, and knew the evidence for it.  He was a creationist,BTW.

There are really smart creationists who can speak knowledgeably about some of these issues.    But there are some prominent creationists/IDers who really don't know what they are talking about.

20 hours ago, Starman said:

Hope you can find someone to play ball on your field, as playing alone isn’t fun.  

one.opinion is, in a number of areas, more informed than I am.   My special interest is in biological systems and functional anatomy.   

[Starman]

Responding to One. Opinion, here are a few thoughts on the subject.  

First of all, some biblical/philosophical observations (I have additional thoughts for a future volley but want to take this one step at a time).

My understanding of evolution is limited, so I will start with what I do know:

In the beginning God created the heavens and the earth. Gen. 1:1

 All things came into being through Him, and apart from Him nothing came into being that has come into being. John 1:1-3

For  by Him all things were created, both in the heavens and on earth, visible and invisible, whether thrones or dominions or rulers or authorities—all things have been created through Him and for Him. He  is before all things, and in Him all things hold together. Col. 1:16-17

Scripture is clear that God is the Creator of all things, both visible and invisible.  Divine creation involves a supernatural, purposeful, directed design process with a specific end in mind (a glorious creation ruled by humanity in the image of God) and, therefore, by definition CANNOT be a random materialistic process.  Since Darwinian evolution is BY DEFINITION a materialistic, non teleological process there is a serious logical inconsistency in the statement God “used Darwinian evolution to create.”  Either the process was undirected and non teleological (no outcome baked into the process) or it was directed and purposeful – both cannot be true. 

The evolutionist claims that the Darwinian processes give biological life the appearance of design, but this is in fact an illusion resulting from the creative power of natural selection acting on random mutations.  What if the more accurate perspective is that the divine process of creation has produced the illusion of an evolutionary process, due the progressive nature of creation (simple to complex) occurring over long periods of geologic time? Evolutionary theory was then developed as the best explanation of the data based on materialistic processes.  Thus Darwinian evolution is in fact the illusion not divine creation.

Question: How does the Christian evolutionist reconcile the idea of Darwinian materialism with  scriptural view that God actively designed and created, since the two viewpoints are clearly at odds?  

[enoob57]

On 2/25/2020 at 9:10 AM, one.opinion said:

I find it more plausible to accept God's direct creation of the first living cells

fine if ya throw out the Bible...

[one.opinion]

45 minutes ago, Starman said:

Scripture is clear that God is the Creator of all things, both visible and invisible.  Divine creation involves a supernatural, purposeful, directed design process with a specific end in mind (a glorious creation ruled by humanity in the image of God) and, therefore, by definition CANNOT be a random materialistic process.  Since Darwinian evolution is BY DEFINITION a materialistic, non teleological process there is a serious logical inconsistency in the statement God “used Darwinian evolution to create.”  Either the process was undirected and non teleological (no outcome baked into the process) or it was directed and purposeful – both cannot be true. 

Correct, if you define evolution as non-teleological, then my view is completely inconsistent with that definition.

46 minutes ago, Starman said:

Question: How does the Christian evolutionist reconcile the idea of Darwinian materialism with  scriptural view that God actively designed and created, since the two viewpoints are clearly at odds?

My belief in God as sole designer and creator cannot intermingle with a view of evolution that is non-teleological. When I say that I believe God used evolution, then I am saying, by implication, that I believe a non-teleological view of evolution is incorrect. I believe God established all creation with the ultimate goal of creating humanity, His created work that could interact with Him.

Sometimes, I remind myself that God is the Creator of time as well as matter, and is not subject to time's flow. To such a Creator, His creation work could be completely established from beginning to end in a single instant, but progress slowly over the span of time.