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The Origin of Biological Information, Part 6

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July 7, 2011 Tags: Genetics

Today's entry was written by Dennis Venema. You can read more about what we believe here.

The Origin of Biological Information, Part 6
If your heart is right, then every creature is a mirror of life to you and a book of holy learning, for there is no creature - no matter how tiny or how lowly - that does not reveal God’s goodness.

Thomas a Kempis - Of the Imitation of Christ (c.1420)

A brief recap of the series to date

This series of posts has been exploring the question of how new structures and functions arise through evolutionary mechanisms. This topic is one that is of considerable interest for Christians, since the Intelligent Design Movement claims that the generation of such features (what it terms Complex Specified Information, or “CSI”) is not possible for natural processes to produce in any significant measure. As such, it holds up examples of CSI in nature as evidence for a supernatural designer. Unfortunately, this approach has the effect that new scientific evidence that explains how CSI arises naturally diminishes the perceived evidence for God.

As we were careful to point out in the very first post in this series, understanding how natural processes create information is in no way a threat to God’s ordaining and sustaining of creation. If it were so, the obvious conclusion would be that “natural mechanisms” and “God’s actions” are effectively a zero-sum game where every scientific discovery diminishes God’s activity. Indeed, the ID argument strongly tends in this direction. This is certainly not a historic Christian view of science, and one we would do well to steer the church away from.

With these theological considerations in mind, we have explored several examples of new CSI arising through evolutionary processes (the posts in this series are linked in the sidebar for those who have not yet read them). In summary, we have seen that:

  1. CSI does not need to arise all at once, but can arise piecemeal through independent mutation events.

  2. Separate mutations that later combine to form CSI do not need to confer a specific advantage on their own. In other words, mutations that are “neutral” with respect to the survival of the organism can later be co-opted into CSI that does have a distinct survival advantage.

  3. Neutral mutations may open up new future paths. For example, the brand-new ability of one bacterial population to use citrate as a food source required that a neutral mutation appear several thousand generations before it combined with other mutations to provide the CSI for using citrate (see Part 2). A second example we observed is how neutral mutations opened up new future possibilities during the evolution of hormone/hormone receptor complexes in vertebrates (see Part 3).

  4. When CSI arises, it can be pretty poor at the beginning. Nascent CSI, though poor, provides a survival advantage because it is the “best game in town” at that time. Further mutation in, and natural selection on, the offspring of the original CSI-holder quickly refine the nascent information into ever-more “specified” CSI.

  5. The detailed examples of new CSI arising through changes to existing proteins appear to apply generally to many, many protein families across multiple organisms (see Part 4). There is nothing about protein structure that prevents proteins from acquiring new functions through evolutionary means.

  6. Comparative genomics evidence, especially evidence from synteny, strongly supports the hypothesis that large swaths of modern vertebrate genomes are the result of ancient whole-genome duplications, where some of the duplicated genes go on to acquire new functions through mutation and selection (see Part 5).

Comparative genomics and new CSI: details, details

One last way to assess the ability of natural processes to generate CSI that we will explore is based on comparing the genomes of two closely-related species that nonetheless have significant biological differences. The most detailed approach, of course, is to examine and compare the entire genomes of the species in question. Such a comparison shows us the total genetic differences that have arisen between the species since they parted ways:

It needs to be emphasized that only a subset of the observed differences will be meaningful. Put another way, many of the mutations that have occurred in the two lineages are neutral, having no discernable effect on the organisms in question. Indeed, the subset of truly meaningful differences is likely to be relatively small. Still, the subset of meaningful differences cannot exceed that of the total genetic differences. So, even if we do not, as of yet, understand all the details of how the species in question came to be biologically different, we can be sure that we know what the upper maximum is for the necessary mutations needed to bring about the differences we observe. So, while the total genetic differences between two species is an overestimation of the genetic changes needed to cause the differences, it is still a useful measure because we know that all of the meaningful changes must be accounted for within it.

Applying this test to humans and our closest (living) evolutionary relative, the chimpanzee, reveals that at a whole-genome level, we are over 95% identical. This value is even an underestimate, since it “counts” mutations that duplicate or delete sections of DNA as if they were separate mutations affecting individual DNA “letters” even though it was created by only one genetic change. Indeed if we use the same criteria to compare the diversity which exists within our own species, we humans are only 98% identical to each other. By whatever measure used, we are but a hand-breadth away from our evolutionary cousins at the DNA level (for those interested in a full treatment of how the human and chimpanzee genomes compare, please see this recent article).

Of interest for our purposes here is the simple realization that a relatively small number of subtle genetic changes undergird the large biological differences we observe between humans and chimpanzees. The increase in CSI associated with building the complex human brain and other distinctively human features in contrast to the body of our cousin, the chimpanzee does not appear to require huge changes at the genetic level. The differences we see, when examining these two genomes, are consistent with small changes,of the sort easily accessible to evolutionary mechanisms. While this observation does not rule out the possibility of God directing this stage of human evolution in a more supernatural way, the genomics evidence suggests that this stage was accomplished in gradual, incremental steps. This observation also matches what we see in the fossil record, with gradual increases in brain capacity, tool making, and other features that mark us out as distinctly human.

Evolution and new CSI: cause for fear or celebration?

So, for evangelical Christians, what is perhaps the most challenging evidence for new CSI arising through evolutionary means comes from within our own genomes. Here we see that, at the genetic level, we are but a stone’s throw from other primates such as chimpanzees. This realization leads to what may be for some an uncomfortable choice: either evolution is capable of generating significant novelty through mutation, genetic drift, and natural selection, or the differences between humans and other forms of life must be seen as insignificant. The only other option is to reject these lines of evidence altogether.

Of course, this response, for many, is one driven by fear: fear of having to re-consider the range of methods by which God creates, or perhaps how one interprets the opening chapters of Genesis. My hope is that this series, while challenging for some, would not ultimately be cause for fear. Indeed, this response plays into the false “natural versus God” dichotomy discussed above. Rather, my hope is that understanding some of the natural means God uses to bring about biodiversity on earth, including for our own species, will provide an occasion to offer thanks and praise to our Creator.


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Mike Gene - #63354

July 15th 2011

Bilbo,

I usually don’t post much here during the week.  

A good start.  How many more to go?  

So far, the score is 3-0.  Three homologs that can be bridged by Darwinian processes and no examples of a homolog that cannot.  

Are you at least willing to concede Axe’s point that being homologous proteins does not necessarily mean an ability for one to evolve by Darwinian means into the other?  

Sure.  But if you recall from the DM, I take a tentative, incremental approach to these matters.  As such, pointing out that X does not necessarily mean Y means very little to me.  

If so, then observing that there is 95% sequence similarity does not necessarily entail that Darwinian processes can account for it.

This is nothing more than arguing it is possible that Darwinian processes cannot account for it.  So yes, there is a possibility that there is some human/chimp homolog out there than cannot be bridged by Darwinian means.  But other than acknowledging the mere possibility, there is no reason to go beyond this.  Again, if someone thinks such a homolog exists, by all means, they should find it and propose it.  

If you try to find one, you’ll end up going through gobs of examples like insulin.

Here’s the amino acid sequence for human insulin:

MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVC
GERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQK
RGIVEQCCTSICSLYQLENYCN

Consider the bolded “A” at position 23.  It stands for the amino acid alanine.  In chimps, it contains serine.  There is no barrier here as a single nucleotide change in the insulin gene bridges these two amino acids.  But what if we consider insulin from orangutans?  Now, position 23 contains glutamine.  Oh, oh.  To bridge alanine with glutamine, we need two nucleotide substitutions.  Yet, one nucleotide substitution could change alanine into proline and a second could change proline into glutamine.  If a proline at position 23 is always lethal in all species, we might have an obstacle here.  But guess what?  If we consider the insulin gene from gibbons, position 23 is occupied by…..proline. 



Mike Gene - #63355

July 15th 2011

Steven,

It is as if Biologos is campaigning to be the next incarnation of intelligent design, with ID terms like “irreducibly complex” being strategically replaced with “mystery”.

Sounds like you a proposing a new conspiracy theory to me.


Steven Curry - #63362

July 15th 2011

Mike Gene, what is the purpose of this comment, other than to troll?


Mike Gene - #63363

July 15th 2011

Are you proposing a new conspiracy theory?  Or are you just trying to imply there is a conspiracy in the works? 


Steven Curry - #63369

July 16th 2011

Mike Gene, on this thread I made a number of substantive comments containing a number of substantive points. However instead of responding to any of those, you extracted a single sentence out of context and made an ad hominem argument. I did not say conspiracy, and you are trying to suggest, by use of the absent context, that I am being paranoid.

I have some license to express my annoyance here because you were also trolling in an earlier thread in which I participated.

You are still welcome to address any of the issues I mentioned in a serious manner, of course.


Mike Gene - #63375

July 16th 2011

Steven Curry.

Mike Gene, on this thread I made a number of substantive comments containing a number of substantive points.

I’ve been making substantive comments about the supposed barriers to evolution while you have been making veiled accusations against Biologos and Jon.  

However instead of responding to any of those, you extracted a single sentence out of context and made an ad hominem argument.

Such boloney.  First, both Dennis and Darrel patiently and sufficiently addressed your accusatorial comments.  You, of course, would have none of it, accusing them of not giving you a “straight answer.”   So you are not likely to treat me any differently.  Second, your “single sentence” nicely captures the context of your entire accusatory “argument.”  In fact, it’s part of your conclusion, immediately following the sentence that begins, “In closing.”  

I did not say conspiracy, and you are trying to suggest, by use of the absent context, that I am being paranoid.

Of course you did not write it.  I never said you wrote it.  I said that your conclusion, “it is as if Biologos is campaigning to be the next incarnation of intelligent design, with ID terms like “irreducibly complex” being strategically replaced with “mystery,” sounds like a conspiracy theory. Because it does.  Rather than deny it, you implied I was a troll.  So I ignored the subtle character attack and asked two simple questions to get you to clarify.  Again, you ignore them and don’t deny you are implying some form of conspiracy.  You reply by attacking me. 

Let’s face it Steve, your conclusion essentially argues that Biologos is “ID’s Trojan Horse.”  That attitude was evident from your whole line of accusations against Dennis and Darrel.   

I have some license to express my annoyance here because you were also trolling in an earlier thread in which I participated.

I see.  So if I focus on a problem with your position, your twice-used defense is to label me a troll.

You are still welcome to address any of the issues I mentioned in a serious manner, of course.

I have no desire to help you resurrect your insinuation that BioLogos is engaged in some strategy to become “the next incarnation of ID.”  BTW, are you a Gnu?  

Now, if you would like to address the issue I raised in #63177, you are welcome to do so.


Steven Curry - #63379

July 16th 2011

Mike Gene: “Are you proposing a new conspiracy theory? Or are you just trying to imply there is a conspiracy in the works?”

I ignored these questions because they are trolling questions—they assume a conspiracy. You might as well have asked, “Have you stopped beating your wife yet?”

The fact of the matter is that the “Leap of Truth” production (http://biologos.org/blog/a-leap-of-truth) makes God-of-the-gaps arguments, as I and others have observed. This should be a major concern. Francis Collins was averse to God-of-the-gaps arguments and he explicitly did not want BioLogos, the organization he founded, to use them. In “The Language of God” Collins writes (p204),

“For the atheistic scientist, BioLogos seems to be another ‘God of the gaps’ theory imposing the presence of the divine where none is needed or desired. But this argument is not apt. BioLogos doesn’t try to wedge God into gaps in our understanding of the natural world…”

I invite you to respond seriously to the points that I or others have made on this thread. Stirring up personal conflict is unwelcome, unproductive, and may even be against the guidelines of this site. Please either address issues substantively or don’t respond at all. Thank you.


Mike Gene - #63383

July 16th 2011

Steven Curry: I ignored these questions because they are trolling questions—they assume a conspiracy.

I see that you still will not deny that you are implying some type of conspiracy where BioLogos “strategically” seeks to become “the next incarnation of ID.”  

You might as well have asked, “Have you stopped beating your wife yet?”

Wrong.  The questions. “Are you proposing a new conspiracy theory?” and  “Or are you just trying to imply there is a conspiracy in the works?” could have easily been answered ‘No.’    Instead of answering no, you have chosen to attack me.  

The fact of the matter is that the “Leap of Truth” production (http://biologos.org/blog/a-leap-of-truth) makes God-of-the-gaps arguments, as I and others have observed.

You are confusing your own subjective perceptions with “the fact of the matter.”  That “others” may agree with you simply means others share in your perception.  Look, are you are Gnu?  And how many of these “others” were Gnus?  This is relevant because if a bunch of Gnu’s believe this, it is not surprising or all that significant.   

I invite you to respond seriously to the points that I or others have made on this thread.

I have responded seriously to the points others have made in this thread (see my discussion of the amino acid sequence of human proteins, for example).  And I invite you to respond seriously to the point I raised in #63177.  I told you I was not going to help you facilitate your attempt to smear the people at BioLogos by giving you a platform to continue with your accusations, especially since you decided to ignore Dennis’s and Darrel’s patient explanations and proceeded to conclude they were strategically setting out to become the “next incarnation of ID.” 


Steven Curry - #63387

July 16th 2011

Mike Gene, I pointed out some of the God-of-the-gaps issues here: http://biologos.org/blog/a-leap-of-truth/CP1/#comment-63036

The first person who responded agreed with me. While that person happens to be a Christian, it’s odd that you think his opinion would not be significant otherwise.

If you wish to make a serious rebuttal (i.e. without ad hominems) to what I or others have said about the above God-of-the-gaps problem, then please do so.

Stirring up personal conflict is unwelcome, unproductive, and may even be against the guidelines of this site. Please either address issues substantively or don’t respond at all. Thank you.


Gregory - #63389

July 16th 2011

These two questions have been asked (in plain English) to Steven Curry: 1) “what’s your own position in the Biologos vision of integrating science and faith?” (Jon) 2) “BTW, are you a Gnu?” (Mike).

As someone who’s been coming to BioLogos blog (with interruptions) from fairly near to the beginning & who strongly supports Jon’s #63386, I’d be assured regarding Steve’s intentions, given that he’s just asked Jon on more than 1 occasion if he ‘supports ID,’ to hear direct answers from Steve to both of the above questions.

& I’d like to add a 3rd & a 4th question:
What ‘positive’ collaboration do you see as possible today between science, philosophy and theology/religion/worldview/spirituality/faith? Do you side with Pierre Teilhard de Chardin or Theodosius Dobzhansky in any ways in your ‘negotiation’ of ‘science’ with ‘philosophy’ and ‘those other things’?

This is a ‘science & faith’ site, quite obviously - just look at the mast-head. We are interested in collaborative and cooperative dialogues. My preference is to people of the Abrahamic faiths, though BioLogos is more concerned with evangelical Christians in particular. Either way, we are not fans of scientism advocacy or warfare mongering here. Logos means more than ‘reason’ alone. Will you reason & more with us?


Jon Garvey - #63538

July 28th 2011

It’s all gone very quiet Gregory. Even the dogs aren’t barking.

An interesting quote from Jame’s Shapiro’s new book, regarding the complexity of the control systems that make up the majority of the difference between human and chimp genomes:

“A little thought will make it clear how difficult it is to maintain
the traditional idea that each individual component of these elaborate
circuits evolves by making its own random walk through the enormous
space of genome sequence
possibilities.”

How come the article makes it sound so easy? I guess it reveals Shapiro’s ignorance of basic biology.


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