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The Origin of Biological Information, Part 4

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April 25, 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 4
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)

Lost in (Sequence) Space

In Parts 2 and 3 of this series (see sidebar), we explored two concrete examples of how new structures and functions arose through mutation and natural selection: the ability of E. Coli to utilize citrate that appeared during a controlled laboratory experiment, and the duplication and divergence of a steroid hormone receptor gene that acquired a new hormone binding partner and went on to regulate new processes distinct from its predecessor.

Both of these examples were notable for their intricate level of detail that carefully teased out the intermediates on the path to new functions. Still, at the close of Part 3 we noted that

Over and against these lines of evidence, however, the Intelligent Design Movement claims that such novelty is inaccessible to random mutation and natural selection. Rather, they claim that functional protein shapes are incredibly rare and therefore so isolated from each other that random mutation and natural selection cannot bridge the vast gulfs between them.

The issue here is that functional proteins seem to be a very small subset of possible proteins. Proteins are chains of repeated structures (amino acids) that are typically one hundred or more repeats in length. There are 20 amino acids found in proteins, so at every position in a protein chain, there are 20 different possible choices. So, for a protein with only two amino acids (not even a realistic scenario) there are 202 possible combinations. For a protein with 100 amino acids, there are 20100 combinations – a vast “sequence space” of possible states, of which only a relative few will be functional.

As we have seen in Parts 2 and 3, proteins “explore” their sequence space through random mutation. Mutation may produce protein forms that reduce or remove function, changes that are neutral with respect to function, or changes that improve function (or add new functions). Over time, evolution predicts that proteins will “branch” through sequence space – with each modern form connected to a previous form of which it is a modified descendant. The Intelligent Design Movement (IDM), as we have noted, predicts a different pattern: isolated, separately designed (created), functional proteins that lack prior transitional forms.

In other words, the IDM views protein sequence space to be like the diagram on the left. The brown spheres represent functional protein shapes (each of which allows for some small variation within the sphere). These are separated by large gaps of nonfunctional sequences. In contrast, an evolutionary model predicts that modern-day functional sequences (brown spheres) are connected in sequence space by functional intermediates across time (black lines).

The two examples we have already examined in parts 2 and 3 (citrate metabolism and novel hormone / receptor pairs; see sidebar for links) are strong support for the evolutionary model: in both cases new functions and structures were connected to prior forms (that had different functions) through a series of functional intermediates. The question remains, however: are all proteins so connected? Are these examples rare exceptions? Certainly if evolution has produced the diversity in protein form and function that we observe today this pattern should be common.

Welcome to the Neighborhood

That was the question that recently led two researchers to examine a large number of protein enzymes with known functions: 28,862 different proteins from a wide array of organisms, to be exact. Specifically, the researchers examined “genotype neighborhoods”: proteins that have similar amino acid sequences and group together in sequence space (such as those represented by the spheres in the diagram above). A two-dimensional cross-section of two such spheres can be represented as follows (redrawn from Figure 2 in Ferrada and Wagner, 2010):

Where each sphere has a radius (r), and the two are separated in sequence space by a distance (d). The radius and the distance are percent differences in amino acids. For example, we may consider all proteins that differ by at most 2% of their amino acids within the two neighborhoods (r=1 for both). The distance between the two neighborhoods (d) is also a percent difference in amino acids (for example, d could be 10%).

Since the data set used by the researchers was for enzymes with known functions, pairs of genotype neighborhoods were assessed to determine if they contained the same enzymatic functions, or distinct functions. For example, if neighborhood 1 contains enzyme functions A, B and C, and neighborhood 2 contains only enzyme functions A and B, then enzyme function C is unique to neighborhood 1. The fraction of unique functions for pairs of genotypic neighborhoods can thus be analyzed as functions of r and d.

In other words, how different do two genotype neighborhoods have to be before new functions are encountered in protein sequence space? Are existing protein families situated in protein space as isolated islands of (independently designed) function in a sea of nonfunctionality, as the IDM predicts? Or can new functions be reached as enzymes explore sequence space through random mutation and natural selection?

Not surprisingly, the researchers found that as the percent amino acid differences (d) increased between two genotype neighborhoods, the fraction of unique functions increased. What was interesting (in terms of assessing the claims of the IDM) was that unique functions can be readily observed even for low values of d. For example, genotype neighborhoods with a 20% difference in amino acids (d = 20) had unique functions over 45% of the time when r was held constant at a 5% difference. Smaller differences, such as d = 10, did not eliminate unique functions (nearly 20% had unique functions; see figures 3A and 3B in Ferrada and Wagner for results for the data set as a whole).

A second interesting result was that even when genotype neighborhoods overlap (i.e. d is less than the sum of the two radii), they still may have unique functions:

This simultaneously underscores two observations: that highly similar sequences may have different functions (as is well known from other studies), as well as the contingent nature of proteins exploring sequence space (even closely related proteins cannot reach the same potential functions via a short search, depending on their position in their genotype neighborhood). This result is also consistent with what we have seen previously in parts 2 and 3: neutral mutations that move a sequence within its genotype neighborhood can bring it into reach of new potential functional states. Such neutral mutations were key in opening up future possibilities both for the evolution of citrate metabolism in E. Coli as well as in for steroid hormone receptors in vertebrates.

Does maintaining a specific protein structure prevent exploration?

Having obtained this result, the researchers went on to add a constraint to the analysis: they restricted their data set to protein sequences known to fold into a specific structure (the data for the TIM barrel domain can be seen in Figures 4A and 4B; compare with 3A and 3B). They chose a very common protein fold (called a TIM barrel) that many protein sequences can fold into (4,132 sequences in the data set), and that performs many different enzymatic functions (53 distinct chemical reactions currently known). The amino acid sequences that form a TIM barrel can be 100% different (i.e. d = 100) or very similar (d ~ 0). As before, the researchers examined how functions are distributed in sequence space for pairs of genotype neighborhoods, but now restricted to this structure alone. Significantly, their results were the same as before. Genotypic neighborhoods close to each other still showed different functions, and overlapping neighborhoods contained unique functions. To be certain that this was not an effect specific to the TIM domain, the researchers repeated the analysis for 36 additional structures, all of which gave similar results.

Put another way, constraining a protein to a particular three-dimensional structure (i.e. protein fold) does not seem to hinder its ability to traverse sequence space and acquire new functions in the process.

Taken together, this paper demonstrates some key findings for how protein sequences, structures and functions are distributed in protein sequence space:

  1. The distribution of protein sequences, structures and functions we observe is strongly consistent with the hypothesis that proteins traverse sequence space and acquire new functions over time through random mutation and selection.

  2. Functional sequences in protein sequence space are distributed such that a significant subset of protein families are close to areas with new functions. In some cases, genotype neighborhoods can overlap where one neighborhood contains functions that the other does not.

  3. Not all areas of a genotype neighborhood are equivalent: neutral mutations within a genotype neighborhood can move a sequence to regions where new functions can be reached, or into areas where those same functions are not accessible.

  4. Constraint on protein structure is not a constraint on acquiring new functions. When the analysis was restricted to a common structure, the same results were obtained (consistent for 37 different structures).

Moreover, this work is based on the largest sample size examined to date (over 28,000 proteins), and thus is much more likely to apply to protein sequence space as a whole than studies (such as those performed by members of the IDM) that attempt to extrapolate from studies of one protein (or a handful of related proteins) to protein sequence space in general. Despite the claims of the IDM, proteins do not appear to be “lost” in sequence space.

In the next post in this series, we’ll examine another line of genomics-based evidence for proteins acquiring new functions over time: the distribution of gene copies with distinct functions (paralogs) in vertebrates.

Further reading:

Ferrada, E., and Wagner, A. (2010). Evolutionary innovations and the organization of protein functions in genotype space. PLoS ONE 5(11); e14172.


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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Christine S. - #58380

April 22nd 2011

This has been an excellent series so far and I do agree with the statements in this post in general.

 

What I found irritating was the suggestion, that in a vast sequence space “only a relative few will be functional”.

There is, to my mind anyway, not enough information available to make any estimate to that effect. To start with, we do not know how many different sequences for any known protein function are currently out there in nature, the number of organisms tested in the lab for protein function is minute compared to what has not been investigated. And the majority of organisms that we would have to investigate to get the full picture are no longer available for testing since they have expired.

 Secondly, we cannot be sure, that the protein functions currently known to us represent all functions that exist today or have existed in the past. Thorntons work that was discussed in the previous entry in this series is an excellent example to show how we attribute functionality to a sequence – by testing the protein for the function. He has made the inferred ancestral receptor and submitted it to functional tests and he has done the same for transitional forms of the receptor. But he clearly pointed out that the function he tested for may not be the function that the ancestor was adapted to best, since it is not known what exactly the ligand was.

Sequence comparison gives us an indication what function to look for in a newly identified protein or ORF, but it does not substitute for performing the actual tests.

In cases where we are not aware of an existing function, today or in the past, we do not have the means to test for it. Sequences that represent proteins exhibiting such a function cannot be recognized as functional. But just because we are not aware of the function of a protein that is part of the sequence space does not make it non-functional.

I am sure, you are fully aware of all this, but in the context of the criticism of IDM, it might be useful to point out, that we cannot positively know that a sequence is non-functional. The absence of known function is not the same as the absence of function. So the small islands of established functionality on the vast plane of sequence space do tell us one thing for certain and that is how little we know.


Dennis Venema - #58617

April 25th 2011

Hi Christine, 


Thanks for the thoughtful comment, and yes, your points are well taken. Biologists do disagree on this issue - some hold that protein sequence space has been fully explored during life’s history on earth, others differ. Adding to the issues you’ve raised above is the fact that proteins function in the context of other proteins (and that we assess protein function in a context of other proteins). So, what appears non-functional to us now may not have been so in the past. 

That said, the paper this blog is discussing does suggest that protein families ( for modern proteins, at least) are, in general, spread out  through sequence space: if you look at their data, the sample size drops as (r) (the distance between two neighborhoods) drops . 

Whether protein space is sparsely populated with function or not, the main point here is we see good evidence for evolutionary connectedness between proteins in sequence space. 

Thanks again for the comment. 

Christine S. - #59140

April 26th 2011

Hi Dennis,

 thanks for your kind reply. I really did not want to distract from the main point of your post and I find it truly amazing that careful analysis of sequence, structure and function can show up the connections between the limited data sets we have.

But Alan has put in few words, what I tried to say
in such a long winded way: The default position concerning protein function in
absence of positive evidence should be >we do not know<. Entertaining the
suggestion that a lot of protein sequences are truly non-functional only give
credence to speculations that proposed multiple steps of incremental changes do
indeed contain non-functional and therefore non-selectable intermediates that
require intelligent intervention along the evolutionary trajectories.
I think
you get the drift

Looking forward to more posts in the series

Christine


Jon Garvey - #59332

April 27th 2011

“Entertaining the suggestion that a lot of protein sequences are truly non-functional only give credence to speculations that proposed multiple steps of incremental changes do indeed contain non-functional and therefore non-selectable intermediates that require intelligent intervention along the evolutionary trajectories.”

But Christine, isn’t entertaining that suggestion, along with the contrary proposition, a necessary correlate of “we do not know”? The alternative is to say, “all the intermediate stages must be functional”. In which case, one could divert ones research resources to areas where the truth is not already assumed.


Christine S. - #62293

June 7th 2011

Hi Jon

 

Sorry for answering so late, but I was very busy and just did not have the time for a carefully worded reply and since I am a bit passionate about protein function I want to make myself as clear as possible.

 

Me: “Entertaining the suggestion that a lot of protein sequences are truly non-functional only give credence to speculations that proposed multiple steps of incremental changes do indeed contain non-functional and therefore non-selectable intermediates that require intelligent intervention along the evolutionary trajectories.”

 

You: “But Christine, isn’t entertaining that suggestion, along with the contrary proposition, a necessary correlate of “we do not know”?”

 

The first thing I would like to point out is, that I wrote “truly non-functional”. This would be a claim that a AA-chain linked by peptide bonds will not interact with anything (binding to something is regarded as function). Since all AA-chains have a functional group at both ends, NH3+ at one and COO- at the other, they are all capable of functional interaction. Additionally the structure of the peptide bond enables them (very short oligomeres excepted) to form complexes with Cu2+, the old standard test for protein content in solutions. So I rule out the “truly non-functional” as an absolute, this is really not on the cards. But this leaves a toned down “non-functional” addressing the question of sequence-specific function.

 

Most people tend to think about protein function in terms of enzymatic activity, structures, interactions in complexes etc., these sort of functions are constrained by maintaining specific binding sites or active centres and other sequence specific features. But this is not always really so important. As an example I would mention albumin – unspecific weak binding to allsorts and found in abundance – it plays a role in drug delivery and influences the viscosity of blood. If we did not know about the role of albumin to start with, we would not consider it as a likely candidate for functionality looking at the sequence. We do not even know about the sequence space that performs a similar function in all contemporary species, never mind the extinct ones. So not very specific functions are very depending on the context. How do you test for something like this? If you have not tested for a very broad function like this, how do you know, that this sequence does not perform a sequence related function? Why would you be justified in claiming, that this sequence does not perform a function at all?


Christine S. - #62294

June 7th 2011

continued

 

But finally getting to your specific point of contention that we should hold “we do not know” as the position to take, when we cannot positively say the protein sequence is functional or non-functional. My point is, that we only assert a protein sequence is “functional” based on positive evidence through performing a test or better a couple of different tests to rule out false positives and false negatives. But the result can be only be interpreted that the one function you tested for is present or not, it does not rule out other functions to be present if you get a negative result. To come to a conclusion that a sequence is non-functional based on functional tests you would have to test for every function under every condition in every sort of context. To rule out all functions by testing is an almost impossible task and I do not think anyone has even tried to do this for even one of the so called non-functional sequences.

 

All we are left with is the absence of evidence for function but that does not allow us to say this is evidence of absence of function (that can only be obtained through a test for non-functionality – a patently absurd concept by the way). That is why I insist that we either know about functionality or we do not know about functionality. And we have practically no way of knowing about non-functionality, so let us not pretend that we can assess protein sequence space by telling functional sequences from non-functional ones. We are merely distinguishing between sequences with reported function, suspected function through homology search and sequences that we do not know any function for.

Claiming that a protein sequence is non-functional is a claim to possess knowledge that simply is not to be had and I would not entertain to make such claims nor to let other go unchallenged if they made such a claims.

 


Jon Garvey - #62311

June 8th 2011

Christine, thanks for your painstaking and clear reply. This makes it clear that the argument, “no function detectable, therefore no function, therefore ID” is a God of the Gaps argument (even if ones ID position doesn’t presuppose God).

Nevertheless, the key issue, not only in ID but amongst “dissenting brethren” in the evolutionary community, appears to be the plausibility of progressive change through randon sequence change and natural selection. If I understand your explanation correctly, it appears to answer that question no more strongly than, “there’s no evidence that it couldn’t happen.”

On the face of it, it would appear necessary to determine in general terms how likely it is that any evolution of a protein between two observed functions could take a path through an array of disparate functions that were not either deleterious or at best, neutral and non-selectable.

Even given the redundancy of the genome, many functions must be positively detrimental to the survival of the cell. If the percentage of detrimental changes is 1%, then evolution by RM and NS is a done deal. If it is 99%, then it appears vanishingly unlikely over a long sequence of mutations and one would, presumably, have to look seriously at the theory.

But without some kind of mathematical basis, or I guess the empirical unravelling of a whole sequence of actual changes and the functions they produced at each stage, is it actually possible to get beyond mere plausibility? In my own field of medicine, we would never dare to cite “Mount Impossible” in a drug trial or epidemiological association.


Jon Garvey - #58510

April 23rd 2011

If it is indeed generally true that the functions of proteins overlap in this way, to form a whole chain of connecting functional sequences, they are truly a remarkable type of molecule. Or to put it another way, life is remarkable adept at finding functions for all the variants.

But is it not the case that for a protein to have function, the genetic mechanisms for control, feedback etc need to be in place so that it is produced in the right quantities at the right place and time? Presumably in general a new function would require a whole new set of higher-level controls to be in place. On the face of it that would seem to introduce a much higher order of complexity than the question of the protein coding sequence alone.


Darrel F - #58904

April 26th 2011

Jon,


 “Presumably in general a new function would require a whole new set of higher-level controls to be in place. On the face of it that would seem to introduce a much higher order of complexity than the question of the protein coding sequence alone”

The story of the evolution of controls is the most fascinating of all and I strongly advise those interested in the subject to read, “Endless Forms Most Beautiful” by Sean Carroll.  At a more technical level, but also extremely profound, is “The Plausibility of Life” by Marc Kirschner and John Gerhart..

The subject at hand here, however, is the evolution of proteins.  Must new functions  be created through supernatural intervention (miracles)  or can they come about through  through the natural laws (God’s customary activity)?  The ID movement has put a great deal of effort into saying that methodological naturalism (i.e. science) has come up short.  Supernatural intervention is required, the leaders say.  Dennis, in this extremely articulate summary of a very complex subject is saying, “Don’t dismiss mainstream science so quickly.”  The gaps proposed by ID leaders likely do not exist.  There is no need to insert supernatural intervention here (complex specified information coming in from outside the system)—not on the basis of some hole in our scientific understanding.

We do have some posts already on the evolution of control mechanisms and we will have more, but for those interested in that, I can’t imagine anything better than Sean Carroll’s book.

Jon Garvey - #58950

April 26th 2011

Thanks Darrel. I second your vote for “Endless Forms Most Beautiful.” Lots of pretty pictures, too.

I still have difficulty getting my head round whether a multi-level system makes it more or less difficult for new functioning (as opposed to functional) proteins to develop. I guess it partly depends on how those levels are organised.

I’d still like to see specific answers on the question of information theory, the basis (of course) of Meyer’s arguments cited in #2 of the series. As I queried there, is the information theory presented wrong in whole or part, or is it inapplicable to biological systems?

In other words it’s not just a question of showing that new proteins appear, but of whether that violates the principles of information theory (in which case the changes are either not truly stochastic or not truly changes of information). If it does violate IT principles, the “why and how” become of some importance, because even non ID guys like Yockey apply them to origin-of-life questions (and as far as I can make out exempt evolution by talking only of Shannon information rather than the less-easily-defined functional information).


Darrel F - #58978

April 26th 2011


It seems to me that it is very easy to get bogged down in language that makes the issue more foggy than it really need be.

Let’s remember the question with which Dennis began this series.   In his book “Signature in the Cell,” Meyer had said that there is no case in which a substantial amount of new complex specified information (CSI) has arisen without the input of external intelligence.  We would say, however, that the parade of life’s history is one long example of a massive amount of CSI arising without the scientifically demonstrated need for supernatural intervention.  

Steve Meyer (Chapter 9, of  “Signature…” for example) and Michael Behe (in “Edge of Evolution”) cite various concrete examples of where they say intervention is needed.   Dennis is addressing those issues here.  He is showing on a case-by-case basis why they (Behe and Meyer) were premature—exceedingly premature—to propose that the issue is solved and that on the basis of scientific investigation, supernatural intervention is required.  Their case, put simply has not been made and Dennis, elegantly, is showing why.

So that’s the biology side of things. 

 For the IT side of things, I encourage interested readers to examine Randy Isaac’s essay http://biologos.org/uploads/projects/isaac_scholarly_essay.pdf , or his blog series on the ASA website http://www.asa3online.org/Book/2010/03/09/id-prediction-3/



Argon - #59614

April 27th 2011

A small aside about the necessity for control, feedback and temporal/spatial regulation with new ‘functions’: Note that most of the core, biochemical reactions that exist predate metazoans and multicellular life. However, in cases where spatial-temporal regulation has been adapted, note also that those control mechanisms are mostly variations on a theme as well. Regulation appears to be one of the more ‘plastic’ or readily changeable features in metazoan evolution.


John - #62335

June 8th 2011

Jon Garvey:

“If it is indeed generally true that the functions of proteins overlap in this way, to form a whole chain of connecting functional sequences, they are truly a remarkable type of molecule. Or to put it another way, life is remarkable adept at finding functions for all the variants.”

What? Neither life nor evolution are. Not all the variants would have function. You’re only looking at the products of selection.

“But is it not the case that for a protein to have function, the genetic mechanisms for control, feedback etc need to be in place so that it is produced in the right quantities at the right place and time?”

Not at all. The most vivid example of this is a series of papers from Oliver Smithies’s lab, in which genes important in hypertension and atherosclerosis were knocked out. 

You have stumbled onto another empirical prediction of an ID hypothesis, though, falsely stated as an assumption. What on Earth makes you think that proteins are only present in the right place at the right time?

Can you see how many, many experiments have directly tested that hypothesis, but would not be labeled as such in the literature, to the great relief of ID hucksters?

“Presumably in general a new function would require a whole new set of higher-level controls to be in place.”

Nope. Why don’t you test your presumption against reality? What happens to your sympathy for ID if it turns out to be false?

“On the face of it that would seem to introduce a much higher order of complexity than the question of the protein coding sequence alone.”

On the face of it? You are talking about your mere presumption, man! Did you see how you just elevated it rhetorically to a fact?

Alan Fox - #58863

April 26th 2011

Dennis:


Whether protein space is sparsely populated with function or not, the main point here is we see good evidence for evolutionary connectedness between proteins in sequence space.

Naive questions. Is there reason to believe that functionality could be the norm rather than the exception. Could not a protein have an undiscovered function in a novel, as yet, undiscovered organism. Why is it supposed that, for any unknown sequence, the default is that it lacks any function? Has anyone made any inroad into the design of novel proteins or has anyone suggested any method of predicting the properties of a hypothetical sequence? 

Christine S. - #59146

April 26th 2011

<i>has anyone suggested any method of predicting the properties of a hypothetical sequence? </i>

You can always calculate
the CSI and compare your bits with the probability bound and if they are not
good enough, take solace in Rich, who assured us, that a negative result can
always be a false negative


Christine S. - #59147

April 26th 2011

Sorry, I have not come to gripps with the formating


Ashe - #58934

April 26th 2011

It looks like the pattern disappears with protein families of single functions. 


In sum, if protein structure equaled function, then all but the most distant genotypic neighborhoods would be functionally homogeneous. Functional neighborhood diversity emerges from the multifunctionality of structures.

Mike Gene - #59093

April 26th 2011

While I understand that most people view design and evolution as mutually exclusive concepts and thus focus on the manner in which this study challenges the IDM, I will once again remind people of a third interpretation – evolution has, in some way, been designed.  And this study seems to fit quite well within the framework of that third interpretation, as it helps us envision evolution as an emergent property of protein biochemistry.  The abstract of the study makes claims that are quite friendly to teleology:

We here characterize the organization of enzymatic functions in protein genotype space, using a data set of more than 30,000 proteins with known structure and function. We show that different neighborhoods of genotype space contain proteins with very different functions. This property both facilitates evolutionary innovation through exploration of a genotype network, and it constrains the evolution of novel phenotypes.

If you have a property, that is intrinsic to life itself, that both facilitates and constrains evolution, you have a viable candidate for guiding evolution.  

Furthermore, there appears to be some type of form to evolution.  Again, from the abstract:

Whether a protein with a given function can evolve specific new functions is thus determined by the protein’s location in sequence space.

In terms of evolvability, this implies that some locations are more special than others.  So is there a logic or common theme to such locations?

As we continue to get a better grasp on our evolutionary history, I suspect we will find there is more to the story than proteins traversing sequence space and acquiring new functions over time through random mutation and selection.  Evolution goes deeper than that.


Mike Gene - #59280

April 27th 2011

Dennis writes,

Over time, evolution predicts that proteins will “branch” through sequence space – with each modern form connected to a previous form of which it is a modified descendant. The Intelligent Design Movement (IDM), as we have noted, predicts a different pattern: isolated, separately designed (created), functional proteins that lack prior transitional forms.

True.  But in what way does the IDM’s “prediction” follow from any conceptual formulation of a hypothesis rooted in our understanding of design, let alone an intelligent design?  

Dennis is entirely correct in describing the “prediction” by placing the word ‘creation’ in parentheses after the word ‘designed.’  In fact, if you think about it, there is no rational justification for using the word ‘designed’ instead of ‘created,” as this prediction is a prediction of special creationism and not intelligent design.  How can I say this?  Consider this quote from the paper:

Structures adopted by many sequences are commonly called highly designable [15], [16]. There has been increasing interest in highly designable proteins due to their use as ‘scaffolds’ in the design of new protein functions [17]. One remarkable example is the zinc finger domain, which is robust to point mutations in alanine scanning experiments [18], and has proven useful in designing new DNA binding proteins [19].

If you think about this, a highly designable protein would have very low CSI.  Yet it is high CSI that is supposed to be the hallmark of design.  So in looking for traces of design through a search of high levels of CSI (proteins that are supposedly beyond the reach of natural processes), the IDM is looking in the wrong places.  An intelligently designed protein would not be fragile and easily break down with mutations, it would be robust to mutations and flexible. 

Just because someone uses the word ‘design’ does not mean they are talking about design.


Dennis Venema - #59569

April 27th 2011

Mike, it’s a shame you don’t have more influence on the ID movement. It’s very refreshing to see someone contemplate design without denigrating mainstream biology or claiming that science is fundamentally flawed. Thanks for contributing. 


Roger A. Sawtelle - #59992

April 28th 2011

It seems to me that we have a strange situation both Darwinians and IDers start out with the same idea of how evolution works, that is by hit or miss random change.  ID says that this will not work and they are right.  The problem then is ID tries to set up an alternate model of how evolution works, which is not correct.

Evolutionists do not defend their original model of change, which basically does not work, but finds other models that do work and explain evolution but than the ID model.  The original model of change thought that nature was stupid, but living things are not stupid, they have a form of nervous system.  They are able to solve problems in creative ways, if not conscious ways.  

Both points of view seem to underestimate the creative power of God to design a universe so specular and good that God does not have to intervene in its workings, yet so delicate and precise that God needs to continually nurse it make sure it runs properly.        

The only problem with this is that it gives dinosaurs like Dawkins the ability to claim that the old model works and base his outmoded ideas on a Theory than never worked. 


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