Behe, Lenski and the “Edge” of Evolution, Part 2: Gaining a New Function

Bookmark and Share

October 23, 2012 Tags: Genetics

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

Behe, Lenski and the “Edge” of Evolution, Part 2: Gaining a New Function

Note: In this series, we reexamine the claim made by Intelligent Design proponent Michael Behe to have found a limit to “Darwinian” evolution in light of recent results from the laboratory of Richard Lenski.

Climbing Mount Citrate

As we discussed yesterday, the most dramatic innovation yet observed in the E. coli Long Term Evolution Experiment (LTEE) was the ability, acquired by one of the twelve cultures, to use citrate as a carbon source under aerobic conditions. When we last discussed the LTEE in 2011, we noted what was known then about the mutations that eventually combined to produce the Cit+ trait:

Tracking down the nature of this dramatic change led to some interesting findings. The ability to use citrate as a food source did not arise in a single step, but rather as a series of steps, some of which are separated by thousands of generations:

  1. The first step is a mutation that arose at around generation 20,000. This mutation on its own does not allow the bacteria to use citrate, but without this mutation in place, later generations cannot evolve the ability to use citrate. Lenski and colleagues were careful to determine that this mutation is not simply a mutation that increases the background mutation rate. In other words, a portion of what later becomes “specified information for using citrate” arises thousands of generations before citrate is ever used.
  2. The earliest mutants that can use citrate as a food source do so very, very poorly – once they use up the available glucose, they take a long time to switch over to using citrate. These “early adopters” are a tiny fraction of the overall population. The “specified information for using citrate” at this stage is pretty poor.
  3. Once the (poor) ability to use citrate shows up, other mutations arise that greatly improve this new ability. Soon, bacteria that use citrate dominate the population. The “specified information for using citrate” has now been honed by further mutation and natural selection.
  4. Despite the “takeover”, a fraction of the population unable to use citrate persists as a minority. These cells eke out a living by being “glucose specialists” – they are better at using up glucose rapidly and then going into stasis before the slightly slower citrate-eaters catch up. So, new “specified information to get the glucose quickly before those pesky citrate-eaters do” allows these bacteria to survive. As such, the two lineages in this population have partitioned the available resources and now occupy two different ecological niches in the same environment. As such, they are well on their way to becoming different bacterial species.

As such, we noted three distinct steps observed by the Lenski group: steps they call potentiation, actualization, and refinement. Potentiation mutations do not themselves result in the ability to use citrate under aerobic conditions, but they are necessary for it to appear later. Actualization is the mutation that first brings about the Cit+ trait, though, as we noted, this step produced only a very weak Cit+ effect. This nascent ability, however, then undergoes refinement through additional mutations and selection to give the final, robust Cit+ trait observed in the culture.

While some things were known about these steps when the Lenski group last published on this topic (in 2008), the precise details remained unclear. What was needed was a complete characterization of the Cit+ bacteria through whole-genome sequencing to help indentify the changes. These long-awaited results are now available in a new paper published last month by the Lenski group, and they shed light on all three stages of the process.

Lights, camera, actualization

The key step - and the one of greatest interest - is of course actualization: the mutation that converted a Cit- cell to a Cit+ one. This is also one of the easiest steps to study, since the mutation provides the cell with a new feature that can be detected experimentally. Though E. coli cannot use citrate as a carbon source in the presence of oxygen, they are capable of using citrate in anoxic conditions (i.e. when oxygen is absent). To do so, they employ a protein that imports citrate in to the cell while at the same time exporting a compound called succinate. Since this protein is already present in the E. coli genome, it was long suspected that a genetic regulatory change that turned on its production in the presence of oxygen could be the key innovation that produced the first Cit+ bacterium in the culture. As we discussed yesterday, Behe notes that this change could result from a loss-of-FCT or a gain-of-FCT mutation:

“If the phenotype of the Lenski Cit+ strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT, it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation.”

Interestingly, the actualization mutation was indeed a change of regulation of the anoxic citrate / succinate transporter, and it arose through a gain-of-FCT mutation. The mutation turned out to be a side-by-side duplication of the citrate / succinate transporter gene, as well as portions of two genes on either side of it. This imprecise duplication placed a partial fusion of these flanking genes next door to one of the copies of the citrate / succinate transporter gene. This brought the copy under the control of promoter sequences derived from of one of its neighbors, a gene that is active when oxygen is present. The resulting product was a copy of the citrate / succinate transporter gene that was now very weakly expressed in aerobic conditions. Since this is an example of a mutation that duplicates a gene and simultaneously creates a new regulatory element for it (causing significant sequence divergence), this is a clear-cut example of a gain-of-FCT mutation.

Responding to the data

While Behe has not yet, to my knowledge commented on this particular development within the LTEE, one of his colleagues in the Intelligent Design Movement (IDM), microbiologist Ann Gauger, has offered her thoughts. Two themes emerge in her commentary: that the Cit+ trait is “not new”, and that the number of mutations it required were within the bounds set out by Behe and another member of the IDM, structural biologist Douglas Axe:

When is an innovation not an innovation? If by innovation you mean the evolution of something new, a feature not present before, then it would be stretching it to call the trait described by Blount et al. in "Genomic analysis of a key innovation in an experimental Escherichia coli population" an innovation [...]

The total number of mutations postulated for this adaptation is two or three, within the limits proposed for complex adaptations by Axe (2010) and Behe in Edge of Evolution. Because the enabling pre-adaptive mutations could not be identified, though, we don't know whether this was one mutation, a simple step-wise series of adaptive mutations, or a complex adaptation requiring one or two pre-adaptations before the big event.

But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E. coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised.

While Gauger does not speak to the tension between her description of the Cit+ mutation as “not genuinely new” and Behe’s criteria that this should be classified as a gain-of-FCT mutation, it is clear that she views this event as within Behe’s “edge” – i.e. within the bounds of “what Darwinism can do.” Additionally, she sees it as falling within the scope of what is evolutionarily possible as proposed by Axe’s work. In the next installment of this series, we’ll revisit how Behe defines his (claimed) limit of what evolutionary processes can accomplish, with this new evidence in hand. In doing so, a careful examination of the potentiation and refinement phases of the Cit+ transition will be informative.

For further reading:

Blount, Z.D., Barrick, J.E., Davidson, C.J. and Lenski, R.E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489; 513- 518.

Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism (New York: Free Press, 2007).

Michael J. Behe (2010). Experimental evolution, loss-of-function mutations, and “The first rule of adaptive evolution”. The Quarterly Review of Biology 85(4); 419-445.


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.

< Previous post in series Next post in series >


View the archived discussion of this post

This article is now closed for new comments. The archived comments are shown below.

Loading...
Page 1 of 2   1 2 »
HornSpiel - #73865

October 23rd 2012

But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use.

Exactly—or the definition of information that you use, both of which seem to me rather nebulous and subjective.

It certainly is an example of reusing existing information in a new context,... But if the definition of innovation is something genuinely new,... then no, this adaptation falls short as an innovation.

Actually this is a pretty good description of innovation in any human context I know of. Was Mozart an innovator? Using this definition No. He took existing forms (symphony, string quartet, opera, concerto) and just improved on them. If that is the way humans innovate, why not call it innovation when the same process ids observed in nature?

But from ID’s perspective then, nothing is original or an innovation. It’s all based on something prior. ID’s restrictive definition of innovation and information disqualifies any natural or human agency that relies on prior information. It becomes a tautology then that an intelegent other is the only source of genuine information and innovation.


RBH - #73867

October 23rd 2012

Gauger writes 


But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E. coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised.


Gauger is playing word games with “innovation.” Since evolution is a process of descent with modification, any “innovation” will be a modification of a previously existing structure or process. “Innovations” do not appear de novo without antecedents (that’s the creationist view, not that of evolutionary biology), and a new structure or process that appears in a population will necessarily have antecedents in ancestral populations. 


Roger A. Sawtelle - #73869

October 23rd 2012

Lenski’s experiments show the hollowness of the claims of the neoDarwinists like Dawkins that evolution has no purpose or direction.

In these experiments the e. coli were placed in a hostile environment which was rich in citrate which they could not use in the presence of oxygen.  It was not that this was not possible, but a change was needed before it could take place.

The point is that some of the e. coli developed the ability to use citrate in the presence of oxygen, while some others developed the ability to make better use of glucose.  These changes, whether innovative or not, were not arbitrary, but were beneficial adaptions to make a hostile environemt into a positive environment for them.

Therefore the e. coli chnaged not as a result from conflict, but because of adaptation to a hostile environment.         


PNG - #73888

October 24th 2012

There is nothing “hostile” (stressful?) about glucose medium with a citrate buffer. And as soon as there are two different genotypes there, they are in competition for the resources available. Try as you might, Roger, you can’t make resource competition, predation, parasitism, etc. go away to suit your philosophy.


HornSpiel - #73895

October 24th 2012

Roger, I certainly hope you are not trying to drive the conflict paradigm into extinction. Both your cooperative ecological niche model and conflict model are useful for gaining insights in the reality of the petri dish. You of all people should agree that not only can they coexist peacefully in the intellectual ecosphere, but that it is a good thing that they do. 

Roger A. Sawtelle - #73897

October 24th 2012

PNG and HornSpiel,

According to the descriptions of the experiment that I have read it was a nutrient poor environment unless citrate was usable.  That is why the change was important. 

In a sense after there was two different genetypes there was no competition because the new one could use the citrate while the original made the most of the glucose.

Give me a good example where conflict drove speciation as opposed to niche adaption. 

Of course humans have a choice as to whether they can live in harmony with their neighbors or not.  Other creatures live in harmony with their environment  based on instinct.  We can work together to seek the truth, or live with the consequences, which is the possibility of our extinction.


Kirk Durston - #73898

October 24th 2012

I cannot speak for Michael Behe, but if what has happened in the LTEE is objectively quantified, it does appear that it is, indeed, ‘not much’ (or to put it more technically, not statistically significant). In other words, the appearance of a novel function may not be statistically significant at all.

As a first step, we need an objective method to quantify evolutionary changes to see if they are significant or not. Neither Lenski et al. nor Dennis Venema provides a method to test the significance of the potentiation, activation and refinement of the Cit+ process. Craig Venter is moving genetics (and evolutionary biology) into the 21st century by emphasizing that living cells are ‘DNA software-driven biological machines’. Treated as such, an information-based approach gives us a method to evaluate evolutionary changes to see if they are significant or not. With regard to genetic information, there are at least three papers that provide methods for measuring functional information/complexity and evolutionary change.

A method has been published to quantify evolutionary changes in terms of functional complexity/information (Durston, Sec. B, Eqn. (8)). In addition to Durston, Jack Szostak and Craig Hazen et al. have also published ways to estimate or measure functional information/functional complexity in biopolymers. For the LTEE experiment, we are not talking about generating functional information (FI) from scratch, but from a pre-existing ground state (Durston). To analyze the LTEE results, we can calculate the change in FI at each of the three phases (potentiation, actualization and refinement). This work should really be done by either Lenski et al, or Venema if there is a claim being made that this is, indeed, climbing a ‘mount’ or is somehow statistically significant. In the meantime, it appears that one or two mutations produced the potentiation step, followed by a possible process of duplication and insertion of promoters for the actualization step. One or two mutations from the ground state represents, at most, 2 bits of FI, and that is assuming only those mutations would have worked, which seems not to be the case from the paper. As for the duplication and insertion of promoters, the duplication of FI creates zero new FI according to the various ways of defining and measuring it already in the aforementioned literature (contrary to popular assumption), but the insertion might.

It is already known that a random search can produce statistically insignificant levels of FI. What Lenski and colleagues, or Dennis Venema need to do, is to show that the FI produced in the LTEE is significant. That is, given what we could expect a random evolutionary search to generate with the LTEE population size, the number of generations, and the mutation rate, is the FI generated a statistically significant departure from expectation values? I don’t think it is, but perhaps they will provide support for their claim.

From a design perspective, I would predict a good organic design must have ‘fuzzy fitness’ boundaries. That is, its ability to survive in as many environments as possible can be enhanced by designing its DNA software to be flexible enough to be capable of exploring nearby FI space to find beneficial adaptations, exactly as we see in the LTEE. Of course, if follows from this design perspective that this will not work to find de novo gene families; those will require novel software modules, which brings me to what I would really like to see Biologos address …. the massive quantum leaps in FI that we observe between certain taxa in the form of de novo, or orphan, genes. For example, we now know there are at least 60 de novo genes unique to humans, not found in any apes. Now that is what I call a statistically significant bit of ‘tinkering’. 

References:

Durston KK, Chiu DK, Abel DL, Trevors JT (2007) Measuring the functional sequence complexity of proteins. Theor Biol Med Model 4:47

Szostak JW (2003) Functional information: Molecular messages. Nature 423:689

Hazen RM, Griffin PL, Carothers JM, Szostak JW (2007) Functional information and the emergence of biocomplexity. Proc Natl Acad Sci U S A 104 Suppl 1:8574-8581


Dennis Venema - #73903

October 24th 2012

Hi Kirk,

Have you read the paper on de novo genes in humans? Are you aware that those sequences are present in other apes as well, but are noncoding? How is it then that you view these changes as “massive quantum leaps” whereas this change (duplication and significant divergence of a gene) is “not significant”? I’m not following your argument here.

Dennis

 


Mazzeratti - #73917

October 25th 2012

Dennis

Thank you once again for a very informative piece. Once again the evidence is clearly there yet completely skewed and misinterpreted to fil the ID agenda.

Waiting with baited breath on Kirk’s response…

M


RBH - #73919

October 25th 2012

I cannot speak for Michael Behe, but if what has happened in the LTEE is objectively quantified, it does appear that it is, indeed, ‘not much’ (or to put it more technically, not statistically significant). In other words, the appearance of a novel function may not be statistically significant at all.”


Writing as one whose doctoral minor was stats  experimental design, I see the phrase “statistically significant” as being used in a distinctly non-standard way there. Does it mean “not very improbable,” or some such gloss?


Roger A. Sawtelle - #73922

October 26th 2012

HornSpiel wrote:

You of all people [emphasis added] should agree that not only can they coexist peacefully in the intellectual ecosphere, but that it is a good thing that they do.

HornSpiel,

This sentence troubles me.  First of all you put in the phrase of all people (which is usually a slam) which does not make sense in this context.  How and where do I indicate that I am against peaceful discussion as against ad hominem war?

Whether people really do coexist peacefully in the intellectual ecosphere is a good question.  I really do not see this in terms Creationists and Darwinists, liberals and conservatives in the USA.  I see intellectual war based on irreconcilable understandings of reality and life. 

As a Christian theologian I see my task as one of reconciliation. (2 Cor 5:18-19)  Reconciliation requires giving on both sides.  When we are reconciled to God, we need to confess our sinfulness and God needs to forgive our sinfulness.

You speak of peaceful coexistence which is a Cold War phrase and not reconciliation.  Peaceful coexistence is being at war without the violence of all out war.  It is better than that alternative, but not a solution as the failure of Communism showns.      


HornSpiel - #73923

October 26th 2012

Roger,

Not trying to slam you at all, though I admit to trying to use a bit of irony to make my point. My point, if it was not clear, is that both a conflict perspective and an ecological cooperation perspective are useful paradigms to looking at reality. For example you said:

Give me a good example where conflict drove speciation as opposed to niche adaption.

Yet the results of the LTEE experiment do seem to be “a good” example. Yes the two strains found ecological niches, but there was a “weeding out.” A process that favored individuals who were either citrate users or glucose efficient. Those who were in between did not survive to reproduce. That sounds to me a lot like conflict, and I think it is a useful way of looking at what happened.

So just as a certain amount of conflict can drive organisms to diverge and in the process create a new cooperative biological ecosystem, so too can ideas diverge. Again I am talking about paradigms or models for looking at the world. Why the single minded focus on cooperation which seems to have blinders on with regard to conflict? It just seems to deny the reality that most people see. Why not admit that both cooperative and conflict perspectives have their place?


Kirk Durston - #73928

October 26th 2012

Dennis Venema wrote:

How is it then that you view these changes (60 de novo human genes) as “massive quantum leaps” whereas this change (duplication and significant divergence of a gene) is “not significant”?

Fair enough. I have asked you to quantify the significance of the process that resulted in the Cit+ trait, so I should be prepared to quantify my assertion as well.

I see the emergence of the functional information encoding the 60 de novo genes described by Wu et al. as a two step process: step one - the appearance of the non-coding orthologous sequences and, step two – the completion of the process in the human genome to produce a functional gene. I would define a quantum increase in functional information (FI) as an increase without the aid of a fitness gradient. In a ‘hill climbing’ problem, there are incremental fitness advantages that, on average, ratchet a solution up the gradient to either a local or global maxima. In this case, the solution is a functional gene. The authors, however, assume the orthologous sequences in the chimpanzee lineages are non-coding. ‘Non-coding’ does not necessarily mean ‘non-functional’, but I think the authors are arguing the orthologous non-coding sequences are non-functional due to their higher mutation rate, which is what one might expect for non-functional sequences (see the ‘Evolutionary Rate’ section of their paper).

If the orthologous sequences in the chimpanzee are non-functional and, by extension, the ancestral orthologous sequences were non-functional, then we do not have the gradual accumulation of FI as a result of ratcheting up a fitness slope over time. Instead, we have the building up of a non-functional sequence via a random walk until it suddenly achieves functionality by a mutational event or series of mutational events in the human lineage. So, to summarize, a quantum increase in FI is observed when a functional sequence emerges from a non-functional sequence without the aid of a fitness gradient.

Quantifying the quantum increase: There is sufficient information given in the Wu paper to allow me to quantify the emergence of one type of de novo gene. First, they mention that no genes that produced proteins shorter than 100 amino acids were considered, so the minimum length of the de novo proteins is 100 aa. Second, the orthologous sequences that would produce predicted proteins shorter than 80% the size of the human proteins were retained as de novo candidates. With these two conditions in place, we can estimate the FI increase for a 100 aa de novo protein for which the Step One portion is 80 aa and the Step two portion is 20 aa. Looking at 35 protein families, the average FI/aa is 2.2 Functional Bits (Fits). (Durston, Table 1) Therefore Step One in our example represents of 176 Fits and Step Two represents 44 Fits. When Steps One and Two are completed, we have a total quantum increase of 220 Bits of FI (or Fits). In comparison, the potentiation phase of the Cit+ trait was a single mutation of a base pair, well within the reach of an random search. I cannot quantify the actualization phase without further information, but shuffling of existing FI to promote an existing gene requires little additional FI. The refinement phase involves no increase of FI using Hazen’s equation.

To appreciate the difficulty of generating 220 bits of FI without the benefit of a functional fitness gradient, solve Hazen’s equation for M(Ex)/N. If I(Ex) = 220 bits, then M(Ex)/N = 10^-66 . That number represents the ‘target size’ of the functional protein in sequence space, or the probability of finding that protein in a single search. For an incremental increase over numerous searches, an upper limit for the number of evolutionary trials over the past 4 billion years is about 10^42 or 10^43. So in my example, we have a phenomenon that an evolutionary search engine falls short of by more than 20 orders of magnitude. By comparison, the Cit+ trait is virtually certain to emerge in far fewer trials, as we observe.

Wu et al. state that the results suggest that an average of roughly 10 novel genes must arise per million years since the split. If a generation is 14 years (chimpanzee), then this translates to 10 novel genes per 71,400 generations. The LTEE is a way to test this. If the Cit+ trait is the most remarkable change we can observe in now over 50,000 generations, should that not give us serious pause for thought?


HornSpiel - #73929

October 26th 2012

Could you give a complete citation for Wu et al.—Thanks


Dennis Venema - #73931

October 26th 2012

“To appreciate the difficulty of generating 220 bits of FI without the benefit of a functional fitness gradient, solve Hazen’s equation for M(Ex)/N. If I(Ex) = 220 bits, then M(Ex)/N = 10^-66 . That number represents the ‘target size’ of the functional protein in sequence space, or the probability of finding that protein in a single search.”

That’s based on the protein popping into existence from scratch, and you could make a similar calculation for any extant protein, whether it originated recently or not. The point of the Wu paper is that we see that these proteins didn’t just pop into existence - there are very similar orthologous sequences in our close relatives. If anything, the Wu paper shows that new proteins can arise as “noise” within a genome -without a fitness gradient- and then some of them go on to come under selection. Also, if you’re going to compare absolute rates between primates and E. coli, you should consider genome size in your comparison. The E coli genome is 4.6MB, but the human genome (as an example primate genome) is 3.2GB.


Roger A. Sawtelle - #73964

October 28th 2012

HornSpiel wrote:

Why the single minded focus on cooperation which seems to have blinders on with regard to conflict?

HernSpiel,

First, let me be clear.  The question has not been conflict or cooperation, but conflict or cooperation.  Darwinism in all its forms has taken the position that Natural Selection is based on conflict, the survival of the fittest. 

If you want to take the position that Natural Selection is based on both, you need to make your case to them. 

Second, Predation and parasitism are not really forms of evolutionary conflict.  Predators and predatees are two sides of a coin, they are interdependent with each other.  Parasites generally benefit their hosts in some way.  The human body is host to billions of symbiotic parasites which protect and empower us.   

Third, competition can have a positive aspect when creatures are competing to be their best.  However war which is the model for Darwinian conflict does not have a positive aspect.  Jesus said that a house divided against itself cannot stand aqnd He is right.

Forth, I made the point that our culture is at war with itself.  Do you agree?

If you agree, do you think that this is good in light of your finding benefits in conflict? 

If you disagree, then do you think that the status quo is fine and no changes are needed?

Fifth, I made the point that what we need is reconcilation.  Reconciliation affirms the real differences and conflict between both sides, but it bridges the gap to enable both sides come together to move forward.

As I understand it this is the Christian mode of resolving conflict.  Maybe you have a different view.                    


HornSpiel - #73989

October 29th 2012

First, let me be clear.  The question has not been conflict or cooperation, but conflict or cooperation. 

????

Darwinism in all its forms has taken the position that Natural Selection is based on conflict, the survival of the fittest.

Is modern evolutionary theory the same thing as Darwinism? My understanding is that it is not. Darwinism is a prejudicial term used primarily by critics of modern evolutionary theory to mis-characterize it. Natural Selection/“survival of the fittest” is only one of several mechanisms that drive evolutionary change. Others include genetic drift and coevolution. see evolution.berkeley.edu/evosite/evo101/IIIMechanisms.shtml.

If you want to take the position that Natural Selection is based on both, you need to make your case to them.

You are mistakenly conflating Natural Selection (which was the primary or only mechanism of Darwin’s original theory) with modern evolutionary mechanisms. Evolutionary theory allows more than the conflict model as a driver of evolutionary change. Your ecological cooperation model fits very nicely into the coevolutionary mechanism.

Forth, I made the point that our culture is at war with itself.  Do you agree?

There are good people on both sides of the culture wars divide. I do not like the conflict. In fact I do choose sides at times, thus becoming a “combatant.” This competition between paradigms can be healthy if it is not overly infected by those (on both sides) who are morally bankrupt. In other words, as long as people maintain honest discussions with personal integrity, such competition can help society come up with better social values and norms. One could cite the civil rights struggle as a case in point. In fact, sometimes a culture war can result in a real war, as in WWII.

In the case of good competition reconciliation also results. But even in the case of bad competition, as WWII, God can bring about good results and reconciliation.


Kirk Durston - #73990

October 29th 2012

Excellent response, Dennis. You have focused on exactly what needs to be discussed.

First, some background information for the sake of other readers who may not be as familiar with this area. At the risk of being simplistic due to word count limitations of this forum, here goes. Roughly 70% of functional proteins have a stable, repeatable and functional 3-D structure which is determined by sequence (Anfinsen). To be a bit more rigorous, the 3-D structure is determined by physics. Most sequences will not give a stable, repeatable 3-D structure, so what an evolutionary search must do is to search sequence space to locate those areas that physics has predetermined to yield stable repeatable 3-D structures. The biological 3-D structures have been superbly engineered and chosen to survive in a hostile environment for countless replications, which means that they can handle a large number of mutations with the result that many thousands of different sequences can code for the same 3D structure. A brilliant piece of design.

What most people do not realize, but the data from Pfam shows, is that these regions of sequence space that code for such 3D structures are extremely sparse. To put it in layman’s terms, if all the sequences coding for a particular protein family  are represented by an island 1 meter square, on average, the next nearest protein family would lie more than 20 million light years away, with most of sequence space representing flat or negative fitness space (the result of which is that natural selection tends to ‘herd’ evolutionary trajectories back into the fold space of the particular protein family). It has already been pointed out in the literature that the non-functional regions between would have to be crossed by a random walk. So you can see that an evolutionary search has a challenge ahead of it, to enormously understate things. With this in mind, let us return to Dennis’ points.

First, as you rightly point out (and which I mentioned in my previous post), Hazen’s M(Ex)/N represents the probability of locating any member of a protein family in a single search but, as both you and I suggested, the location of a novel protein family may be an incremental piecing together of a potential functional sequence in the random ‘noise’ of a flat fitness gradient (it is actually negative, as the extra non-functional baggage has its own energy cost, but we will ignore that).

Where I think you walk into a dead end is your assumption (which is almost universal in evolutionary biology) that the probability of a novel protein family popping into existence from scratch is less than the probability of it incrementally being built within the random ‘noise’ of a flat fitness space. It is quite the opposite. The probability of it popping into existence from scratch on some non-coding stretch of DNA is Hazen’s M(Ex)/N (or, at best .662^N where .662 is based on data which indicates that an average of 4.3 aa/site will be functional.). But the probability of it coming into existence via a random walk is approximately .662^N(N!/N^N) which you can see is many orders of magnitude less probable (N!/N^N is much less than 1 for an average protein length).

Second, as you correctly point out, the hominid genome is much larger than the E. coli genome. However, the number of E. coli involved in the LTEE, at any time, is likely to be a few orders of magnitude greater than the theoretical hominid population was. Of course, this may present problems as far as fixing mutations in a larger population, but I think the LTEE is using multiple, separate populations and I would hope controlling population size to compensate for this.

Finally, you suggest that the Wu paper shows that new protein families can arise from the ‘noise’ within a genome, without a fitness gradient. My response is that such an hypothesis needs to be tested. We can do it computationally, in which case it is overwhelmingly falsified, or we can test it in the lab (i.e., the LTEE). I would say that if after 50,000 generations, the most impressive thing to happen is an utterly trivial mutational event producing the Cit+ trait, then we are well on our way to falsifying this hypothesis in the lab.

Science is consistently falsifying the notion that blind and mindless natural processes can write computer code. It is an empirical fact that intelligent minds can. Thus, functional information is a positive ‘fingerprint’ or marker of intelligence. The fingerprints of intelligence are all over the genomes of life. This is not an argument of ‘we don’t know what did it, therefore God did’. Rather, it is ‘we know what can produce statistically significant levels of functional information ….. intelligence can, and the genomes of life are filled with functional information.’


Roger A. Sawtelle - #73992

October 29th 2012

Coevolution is likely to happen when different species have close ecological interactions with one another. These ecological relationships include:

  1. Predator/prey and parasite/host
  2. Competitive species
  3. Mutualistic species

HornSpiel,

Thank you for this quote from the webpage which you gave.

First of all, as far as I know Dawkins, Dennett, and Co. proudly proclaim to be disciples of Charles Darwin and build their thought both scientific and philosophic on this ideas concerning evolution.  Therefore I am not using the term Darwinism in a negative sense, but in a way that these evolutionists use it. 

Second, thank you for this quotation, which indicates that Natural Selection is now called coevolution.  This does follow in that Dawkins uses the example of the “coevolution” of a wasp and fig tree as a spectacular example of evolution at the climax of his most important book on the philosophy of evolution, Climbing Mt. Improbable.        

Dawkins and other evolutionists have been against ecology, as clearly demonstrated by their fight against L. Marguilis and J. Lovelock.  But as this quote indicates “coevolution” or Natural Selection is based on ecological relationships.

Now this is what I have insisted upon from the beginning and have been denied repeatedly by people on all sides of the question.  If you doubt that this is my position I refer you to my book, DARWIN’S MYTH.

There fore it seems to me that modern evolutionary thought has caught up with me, rather than I need to catch up with it.  The only problem it seems is that evolutionary biologists do not want to give ecology the recognition it deserves.  Evolutionary  as been seen as a biological process.  Ecology is broader than biology, and Ecological evolution is broader than biology. 

WW2 had some good results despite over 95 million deaths it caused, because the “right side” won.  However it also lead into the Cold War which cost over 50 million deaths.  Can we endure another century like the last one?  

Right now we are not fighting against an absolutist racist ideology or an absolutist toltalitarian ideology.  We have the struggle between modern absolutist dualist worldview against postmodern relativist monist worldview. 

They are clearly incompatible.  They are clearly not totally right or totally wrong.  That is why we need a reconciliatory third alternative worldview to enable us to move forward and not allow an absolute non-western world view like Islam to take over.         

 


HornSpiel - #73993

October 29th 2012

Second, thank you for this quotation, which indicates that Natural Selection is now called coevolution.

I am not sure that is what the website is saying. On the page to which the first link I gave above points, the two are differentiated. In any case I am glad these definitions are useful. I thnk our differences on these things may be more semantic than actual.

However you wrote:

War which is the model for Darwinian conflict does not have a positive aspect. 

And also:

Right now we are not fighting against an absolutist racist ideology or an absolutist toltalitarian ideology.  We have the struggle between modern absolutist dualist worldview against postmodern relativist monist worldview. [emphasis mine]

So are you including yourself in the We? If so why? If war, which fight and struggle imply, has no positive aspect?

If not, are you not struggliing for or fighting for a third alternative? Certainly the “struggle between modern absolutist dualist worldview against postmodern relativist monist worldview” is not a literal fight but intellectual, and under the radar of most individuals. It seems to me also, that it’s the normal and healthy way for people and societies to deal with their differences.

 


Roger A. Sawtelle - #73994

October 29th 2012

HornSpiel,

Forgive me for overlooking the explanation of Natural Selection found in your Evolution 101, which demonstrates how silly the Darwinian conflict view is.

First it posits a mixed population of green and brown beetles.  That is completely wrong.  You must start with a uniform population of say green beetles.  Then variation causes some beetles to be brown.  If the brown beetles are better camoflagued then they will survice and the green will die out. 

However how would the green beetles come into existence in the first place if they were easy pickings for the birds?  More likely the green beetles will continue to flourish in ecological niches where green coloring is good, and brown beetles will flourish those niches where brown coloring is good.

That is why ecology is determinant.  This why natural selection and evolution as difined by non-ecological thinking that most people espouse is wrong and leads to all kinds of wrong conclusions. 

Please stop trying to excuse bad thinking, which is trying to bring two mutually exclusive ways of thinking into agreement, and try to solve the real problem, which is trying to find a viable alternative.        


HornSpiel - #73996

October 29th 2012

However how would the green beetles come into existence in the first place if they were easy pickings for the birds?

Roger, do you accept common descent of the species? If so, the way in which various colors came about would be the same, except less extensive. See this page and its nine subpages

One scenario would be that populations of the beetles, say originally brown, became geographically separated and in on location green was more protective so eventually green beetles came to dominate. This does not mean that the brown variety completely disappeared as a trait that could be expressed. Moreover, suppose an event happened that remixed the populations in an environment where neither brown nor green was strongly selected for. Now you would see a well mixed population.

Nevertheless I do not disagree with your basic premise that ecological factors must be considered in order to understand the direction that evolution will take. In fact, one of the ways that God could guide evolution would be in the providential ordering of such ecological events.

Please stop trying to excuse bad thinking…

I don’t think I’m making excuses. I simply do not see that you have presented a pervasive case of bad thinking in the scientific establishment that “needs a viable alternative.”


Roger A. Sawtelle - #73999

October 29th 2012

HornSpiel,

Wake up and smell the coffee.  Ecology guides and determines evolution. 

When life began on earth, a long time ago, the environment of the earth was fairly simple and uniform.  Since then the environment has become more complex and diverse.  Guess what?  Life forms also have also become more complex and diverse.  Is this a coincidence based on random mutations, or the result of ecological cause and effect?

One important study done not too long ago demonstrated that the opening of new ecological niches seemed to result in the development of new species.  Again one cannot say for certain that that there is a direct cause and effect relationship, but I think that this is a reasonable conclusion except to those who have an ideological bias against it.

The scientific establishment claims that life has no meaning or purpose.  The prime basis for that reasoning is Darwinian evolution.  The question is, Is this true?  Christianity clearly says that life does have meaning and purpose. 

So, which is right, Christianity or Science?  If you think that Science is right, then no new understanding is needed and we can throw Christianity in the trash.  If Christianity is right we need new scientific thinking and evidence indicating that life does have meaning and purpose, which in my opinion already exists if people are willing to consider it, instead of dancing all around it.

Why are Christians so reluctant to criticize materialism?               


HornSpiel - #74009

October 30th 2012

The environment has become more complex and diverse… Life forms also have also become more complex and diverse.  Is this a coincidence based on random mutations, or the result of ecological cause and effect?

Both. It is exactly what one expect in any ecosystem. However I maintain that God is sovereign over coincidence and what Science can only describe as random or probabilistic events.

One important study done not too long ago demonstrated that the opening of new ecological niches seemed to result in the development of new species.

This is exactly the what current evolutionary theory, as I understand it, predicts.

The scientific establishment claims that life has no meaning or purpose.

That is a philosophical question outside the bounds of evolutionary theory—I think we both agree. The way to deal with it is to continue to educate the public that, from a proper understanding of science in general and evolution in particular, that such claims are baseless.

If Christianity is right we need new scientific thinking and evidence indicating that life does have meaning and purpose

This is where I think we disagree. I could agree that we need “new” scientific thinking, if you meant by that an better generally accepted understanding of science. But I don’t think you do. You feel the philosophical basis is flawed, I disagree. We have been through that.

However you have said something here I see as “new.” You say we need new scientific  evidence that life has meaning and purpose. I don’t recall you saying that before. It sounds a bit like ID. But then you say that that evidence is already dancing around us. So you are not actually saying we need new facts or data, you are saying that we need new lenses with which to look at life. And with them meaning, purpose, and by implication God will suddenly come into focus. The blind will see. And all this will be the result of doing Science right.

Have I understood you? If so, I not only have scientific but theological objections as well.


Kirk Durston - #74010

October 30th 2012

Correction: In my previouis post, the value .662 should be replaced with .215. The value .215 is the ratio of the average number of functional aa/site (4.3) divided by the total possible (20). I was doing some work with logirithmic equations and accidentally typed in the -log of .215, which is where the .662 came from.


Roger A. Sawtelle - #74013

October 30th 2012

HornSpiel wrote:

That is a philosophical question outside the bounds of evolutionary theory—I think we both agree. The way to deal with it is to continue to educate the public that, from a proper understanding of science in general and evolution in particular, that such claims are baseless.

Dawkins claims that that Darwin’s Theory of Evolution proves that there is no God.  I agree if Darwin’s theory particularly his understanding of natural selection were correct.  That is a philosophical/theological conclusion based on a supposed scientific fact. 

Are you saying that scientific facts have no impact on philosophy and theology?      

HornSpiel, I thought you had been around this blog long enough to get some understanding of what I am trying to day, but guess I was mistaken.  I wroter a long essay more than a week ago in response to a question you asked, I don’t think you responded.

The problem is the one I outlined above.  We have two conflicting views of reality, monism and dualism.  Both are flawed, but contain some truth, so we are caught in a cycle that neither side can win. The only solution is to look beyond monism and dualism to a new one which is inclusive of the best of both and can offer a solution to many of our intellectual problems.   

Now let me have your scientific and theological objections.


Roger A. Sawtelle - #74031

October 31st 2012

However I maintain that God is sovereign over coincidence and what Science can only describe as random or probabilistic events.

So it is random that there are 365.25 days in a year?  It is random that 2 + 2 = 4?  Are time and space random?  Are the laws of nature random?  Is the fact that the universe is a cosmos random?  Not if you mean that there is a probability of 100% that these facts are true. 

It sems that maybe you have bought into the lie that Science can only describe events rather than understand events.  That indeed was the view of ancient science which was content to map the movement of the planets, as opposed to Copernicus who was able to understand the movement of the planets in terms of laws and a helocentric model of the solar system.  These folks want to set science back more than a thousand years, which is an important reason why Scientism is very dangerous and scientists must not buy into their worldview even though they label it scientific.    

The future of the earth depends on ecology.  This is quite evident in the aftermath of superstorm Sandy.  Evolution does not care about the future of the earth, in that it says that the earth can take care of itself.  Any concern regarding how humans are impacted by climate change is seen as species-ism.

Evolution teaches that it is every species for itself and it really makes no difference what happens in the future.  Ecology teaches that humans live in an interdependent world so what humans do affects other species and the well being of other flora and fauna impacts on our future as well as how we change the environment.     

Evolution has taken over some of the language of ecology, but not the model of ecology.  But it is the model that is most important.  Survival of the fittest is the problem.  Social Darwinism is the issue.  As long as this view is endorsed by Science Western thought, it is moving in the wrong direction, that is away from Christianity.  Of course ironically much of conservative Christainity has accepted and supports the tenents of Social Darwinism, so its not the labels we use, but the models we practise and espouse.       


Roger A. Sawtelle - #74049

November 1st 2012

Moreover, suppose an event happened that remixed the populations in an environment where neither brown nor green was strongly selected for. Now you would see a well mixed population.

HornSpeil,

You answer your own question in such a way that demonstrates that I am correct. 

It is the environment or ecology that determines which colored beetles are selected in and nothing else.  Natural Selection equals ecological selection and nothing else.  Evolution is not random, evolution is determined by the environment.  


Jon Garvey - #74181

November 6th 2012

Well, it’s eight days since Kirk Durston replied to Dennis, and it looks as if the pattern of non-reply to challenges from Bioinformatics over the last couple of years is set to continue. That’s a shame as even someone like me with only basic reading in information theory from the likes of Yockey and so on can see the issues involved, so the silence comes across as rather anti-intellectual.

I do hope that it’s nothing to do with Beaglelady’s suggestion that Durston is a “creationist” unworthy of debate - that would be a little too much of a leaf out of Dawkins’ book. Maybe it’s just that people are ill-informed on bioinformatics, but then one should admit it and move on (hopefully to getting better informed).

For anyone waiting this seems suitable and pleasant background music.


beaglelady - #74198

November 6th 2012

I pointed out that he is a creationist. I never said he was unworthy of debate. If he really wants to debate science, why is he on a blog that is mostly about religion?  


Eddie - #74202

November 7th 2012

What you said under Ted Davis’s column, beaglelady, was:

So why on earth would I want to listen to the creationist Captain James T. Kirk Durston?”

Any normal English-speaker would interpret that comment exactly as Jon Garvey did above.  

As for your question, it is startling how off-base it is.  The column above is about science, not theology, and in it Dr. Venema makes scientific, not theological, claims.  Kirk Durston responded because he disagreed, as an active research scientist, with some of those claims.  It was perfectly appropriate for him to “debate science” in this spot.  Where else would you expect someone to comment on the scientific contents of a BioLogos column, but underneath that column?  And where else could a reader of BioLogos follow the debate more conveniently?

For my money, there should be more debates of this sort under the scientific columns here.  Both men have displayed biological knowledge, and the debate has been polite, focusing on substance, not on personalities or alleged motives.  This is how ID and TE people should interact, with civilized arguments, not sniping.  I’m looking forward to Dennis’s speedy recovery, so we can read more of the thoughts of these two Christian scientists as they have a rational debate about evolutionary mechanisms.  Aren’t you?  Or have you already decided, that, since Kirk Durston is a “creationist captain,” you can’t possibly learn anything about evolutionary biology from his arguments?


beaglelady - #74214

November 7th 2012

You took my quote out of context, Eddie.   I mentioned that I have good opportunities where I live, and had no reason to listen to a creationist who doesn’t have a very good reputation among scientists that I can see.     

Steve Matheson, a Christian, has debated him on this very forum and found him to be wanting.  Wesley Elsberry, another Christian, has explained Durston’s misrepresentations on his own blog here:

http://austringer.net/wp/?s=durston

But if you you guys want to hail him as a great scientist doing cutting-edge research, go ahead.  

 


Eddie - #74218

November 7th 2012

No beaglelady, there was nothing “out of context” in my inference of a sneer against a person you consider a “creationist.”  No one who has read large numbers of your posts here could miss the edge there, especially pointed with the mocking play upon “Captain Kirk.”  If all you had wanted to say was that you had heard more experienced scientists elsewhere, you wouldn’t have stuck in the words “creationist Captain” the way you did.  

Dismissing someone’s argument on the basis of personal information that does not come into the argument (in this case, the fact, if it is a fact, that Durston is a “creationist”) is a logical fallacy known as “ad hominem.”  I suggest that you look up the term, and familiarize yourself with it.  Nothing in Durston’s argument here in any way depends upon his private religious beliefs.  Have you even read what he has written, before taking up arms against it?  

As for Elsberry, you are so predictable!  You pick someone whose biases match your own, and whose partisanship in these debates is extreme.  He is a co-founder of Panda’s Thumb, a virulently anti-ID site, and he works for the NCSE, a Darwin-only propaganda institute.  He appears to have no regular academic position at any recognized university, and it is not clear from any online biographies I’ve found that he ever held any such position.  And his specialty (according to the same biographical sources, none of which link to any c.v., so I can’t see what articles he has published) is marine biology, whale sonar and the like, so he is not even in Durston’s field (biological informatics).  So there is no reason to believe that he would be competent to comment on Durston’s arguments here.

As for Matheson, I already challenged you to produce of list of his peer-reviewed articles in secular evolutionary biology journals.  That was days ago, and there was only silence from your end.  And of course, Matheson, as any reader of his blog knows, is himself highly partisan and lacking a calm, dispassionate attitude toward these debates.

The point, beagelady, is that Durston is offering arguments here, and you are in effect saying that you don’t need to respond to them, or even read them, because you’ve heard from someone else that Durston is not reliable. You are arguing based on authority—and such arguments have no rational status.  You should argue based on your own personal knowledge.  Either refute Durston’s arguments, or stop speaking against him based on your tribal allegiances.  Do the honorable thing, instead of the partisan thing.

Notice that Dennis here has responded to Durston’s contents.  He has not used any of the kinds of unscientific, unscholarly methods of argument against Kirk that you are employing.  Dennis is arguing honorably.  I would suggest that you use him as your role model.  


beaglelady - #74264

November 9th 2012

If you have problems finding research papers by people like Wesley Elsberry,  etcl, why not consult a research librarian to help you out? 

Do you consider yourself not highly partisan?

 


Eddie - #74266

November 9th 2012

It’s not up to me to prove that Elsberry has publications in biological informatics; I’m not the one citing his opinion against Kirk Durston.  If you  know of his publications in that area, let’s have them.  And if you don’t know of any, how do you know that he is capable of refuting Durston in Durston’s own field?  And if you don’t know that, then your choice to side with Elsberry is purely because he is on “your side” rather than because he is competent.  That’s what I mean by saying that you are partisan.

No, I’m not highly partisan.  I haven’t said that Kirk is right or that Dennis is wrong.  I’ve stated that Dennis and Kirk are having a good debate, and that there should be more balanced, polite ID-TE debates like it on this site.  You, on the other hand, have dismissed Kirk’s position without discussing even a single one of his points (if indeed, you have even read anything he has written here), on the grounds that he is a “creationist.”  So you are the partisan one, it seems.    


GJDS - #74203

November 7th 2012

Beaglelady, perhaps you can straighten me out by pointing to the major theological questions discussed in this blog - and I do not mean if God tinkers with evolution, or he waves his hands magically to sustain the poor old universe when it needs such sustaining.

Durston seems to have pointed to some interesting science (how direct he is in this, I do not know) when he refers to the ‘physics’ and the 3D structure(s). These type of reaction routes usually need to be considered within the Gibbs equation, and I think both the enthalpy and entropy terms will give these bio-evolutionists a few questions (the entropy term may not be favourable for highly ordered 3D molecules).

But perhaps this too is too much like science; perhaps first we should identify your theological questions and the solid basis for them?


beaglelady - #74215

November 7th 2012

Maybe Durston should concentrate on convincing other scientists first?


Eddie - #74221

November 8th 2012

He is trying to convince another scientist—Dennis Venema—right in front of your eyes!  Have you followed the dialogue between the two men here at all?

Sheesh.


beaglelady - #74228

November 8th 2012

What I mean is that scientsts communicate their ideas through peer-reviewed journals and conferences.   It’s not quite the same thing as wandering in and posting on a religion blog. 


Eddie - #74242

November 8th 2012

An argument is an argument, no matter where it was posted, on a blog site or in a peer-reviewed journal.  Either you can refute what Durston says here, or you can’t.

But if you insist on dealing only with peer-reviewed writings, try this one:

http://www.tbiomed.com/content/4/1/47

Refute that one, if you’d rather.

But of course you won’t.  You never do.  You simply make endless arguments from authority.  And mostly from poor authorities—washed-up scientists, scientists turned political activists, fired scientists, scientists without their Ph.D.s completed, scientists whose field is not evolutionary biology (and in some cases not biology at all), etc.  But it’s not legitimate to argue even from good authorities.  One has to argue from the evidence.  If you can’t do that, you shouldn’t be making any comment on the views of Durston at all.


beaglelady - #74262

November 9th 2012

I still maintain that scientsts communicate their ideas mainly through peer-reviewed journals and conferences.  This carries more weight than an exchange on a religious blog that not too many scientists follow.  

I have good reason not to trust Durston.  The people I mentioned are trustworthy—especially a certain acclaimed professor at an ivy league university. Your characterization of them is very telling.  Maybe John Polkinghorne is washed up—after all, he left his career in physics and became a priest.

You are welcome to hail Kirk Durston as someone doing cutting-edge research. 


Eddie - #74267

November 9th 2012

Your comment about John Polkinghorne shows a shocking contempt for clergymen in relation to scientists.  I certainly never said that he was “washed up” as a scientist—he was not one of the TEs I had in mind when I used that phrase.  But if I did think that, which I don’t, it would be based on his performance in science, not on the fact that he became a priest, as if that is somehow an intellectual step down from doing science.

You have given no reason at all not to trust Durston, beyond your personal prejudice against creationists.  In any case, “trust” is irrelevant in science.  You are not being asked to lend Durston money, or share national security secrets with him.  You are being asked to evaluate his arguments.  And that you will not do.  So you’ve opted out of the scientific discussion, and that renders your personal opinion of Durston’s arguments of no relevance.


beaglelady - #74270

November 9th 2012

I have no “shocking contempt” for John Polkinghorne—quite the opposite. You are deliberately putting a spin on my statements. I gladly went to hear him speak in my church and had dinner with him.  I felt SO privileged; it’s hard to describe that evening. He is a great scientist and a  great clergyman. 

So who is washed up as a scientist? 


Eddie - #74273

November 9th 2012

I didn’t deliberately put any spin on your statement.  I interpreted it exactly the way it sounded to me, the way I would have interpreted it if my best friend in the whole world had said it.  You wrote:

“Maybe John Polkinghorne is washed up—after all, he left his career in physics and became a priest.”

Which certainly sounds as if you think that being a priest is an intellectually lightweight job that a physicist might turn to once he realizes his brain is no longer capable of doing serious scientific thinking.  You may not have meant that, but that’s what it honestly sounded like to me.

I would say that people who have not published technical scientific books or articles in a decade or more are pretty well washed up as scientists.  You draw your own conclusions.  But Kirk Durston is certainly not washed up.  He is more like revving up, for a promising career.  

 


beaglelady - #74275

November 9th 2012

Again, who are these washed-up scientists you speak of?


Eddie - #74268

November 9th 2012

P.S., beaglelady:

Your point that scientists should use peer-reviewed journals and conferences to communicate, rather than blogs, etc., shows your double standard.  You’ve never complained when many atheist/agnostic scientists over at Panda’s Thumb or Pharyngula or Sandwalk have made arguments in those non-refereed venues (if you do a word count, I think you will find that P. Z. Myers and Larry Moran have published more about evolution on blog sites over the past ten years than they have in papers read at scientific conferences or published in peer-reviewed journals), and you’ve never uttered a peep of protest when TE scientists such as Karl Giberson, Darrel Falk and Dennis Venema have made arguments in columns in the non-refereed environment here, or when TE Steve Matheson made arguments in his own non-refereed blog (and I’m still waiting for that list of Matheson’s peer-reviewed papers in evolutionary biology from you, by the way).  Nor have you complained when TE Ken Miller has published his refutations of ID in books by trade presses rather than in peer-reviewed scientific journals.  It is only when ID people argue in such venues that you raise your great principle that scientific arguments belong in peer-reviewed journals and conferences.  Oh no, beaglelady, you are not partisan at all.


beaglelady - #74269

November 9th 2012

 Your point that scientists should use peer-reviewed journals and conferences to communicate, rather than blogs, etc., shows your double standard.

Actually, what I said was this:

I still maintain that scientsts communicate their ideas mainly through peer-reviewed journals and conferences.

This means that the main way scientists communicate their ideas is through peer-reviewed journals and conferences. They publish in the journals that other scientists are reading, and start the ball rolling.   I never said they should refrain from writing popular books and blog articles. 


Eddie - #74272

November 9th 2012

If that’s what you meant, beaglelady, then you have no complaint against Durston, since by your own admission he has published some peer-reviewed articles.  And he has posted comments here only infrequently.  So he meets your criterion of publishing his scientific work mainly in academic venues.

And if that’s what you meant, why haven’t I heard you complain about the fact that Ken Miller has mainly (in fact, exclusively, if my information is correct) —published only popular books, popular talks, etc. since Finding Darwin’s God?And based on my own count (of peer-reviewed science articles vs. columns here and talks at churches and Christian conferences, etc.), a number of BioLogos columnists would fall afoul of your rule, since they publish almost exclusively non-refereed material, here or in specifically Christian journals, and relatively little in secular scientific journals or at secular scientific conferences; yet I haven’t heard you lecture any of them for that.  And Eugenie Scott has written lots and lots of popular stuff for the NCSE web site for years now, while publishing—unless I’m wrong—nothing in her field of anthropology, but she still ranks high in your estimation.

Meanwhile, Jonathan Wells and Paul Nelson, who avoid blogging, presented a joint poster session at a mainstream biology conference last year, and Rick Sternberg, who has many peer-reviewed articles, almost never writes popular articles, and Gauger, Axe, etc., are busy publishing scientific articles and editing a journal, and rarely comment in popular forums, and Michael Denton publishes articles in scientific journals all the time, and never engages in internet debates or blogging, and Behe has used blogs mainly to respond to technical scientific criticisms of his books, and otherwise does his own research—he had a major literature review in a respected secular biology journal last year.  But I don’t hear you praising these ID folks for minimizing the popular stuff and focusing mainly on getting their work out to the scientific community.  So the double standard is still obvious.

But let’s get back to basics, beaglelady.  This all started when you tried to dismiss Kirk Durston, implying that there was no need for you to read his arguments because he was a creationist.  And after all the verbal fencing, you’ve still not said one word that indicates to me that you have read Kirk’s comments here, and not one word that indicates you have read the technical scientific article that I linked you to (the sort of article you say earns your respect).  It’s clear you don’t want to deal with the substance of Kirk’s argument at all.  Why don’t you just admit that you’ve already decided that Kirk’s conclusions are wrong, in advance of reading his arguments?  And why can’t you own up to the fact that such prejudice—pre-judice, literally—is something that no one claiming to defend “science” should harbor in her soul?


beaglelady - #74276

November 9th 2012

Ken Miller has published many articles in prestigious journals.  

Eugenie Scott probably no longer has time to do research, as she is an advocate for science education.

I will watch this debate and see how Dennis Venema answers any objections.   He has left a question for Durston, as a matter of fact.


Eddie - #74279

November 9th 2012

“Ken Miller has published many articles in prestigious journals.”

That was never in dispute.  The question I have implicitly asked you, which you continue to duck, is whether he has published any since Finding Darwin’s God in 1999.  Since you seem to have so much material favorable to atheists and TEs and your fingertips, I assume you would tell me if he had.  I’ll take silence on your part as confirmation of the report that he hasn’t.

Eugenie Scott has every right to swap the life of a scientist for the life of a political advocate.  It’s a free country.  But if she’s hasn’t done any scientific research in years, then she’s hardly in a position to evaluate cutting-edge research in bioinformatics, is she?

Still waiting for your list of Matheson’s peer-reviewed publications in evolutionary biology, and your list of Elsberry’s peer-reviewed publications in evolutionary biology, and your list of his previously-held academic or research positions.

Still waiting for your explanation for your disrespect for the peer-reviewed publications of Behe, Sternberg, etc.  Still waiting for your explanation of your silence regarding those TEs who mainly communicate through popular articles rather than peer-reviewed journal articles or scientific conference papers.

You’ve committed yourself to “watch the debate” with Durston.  But that’s a rather vague statement.  You’ve indicated that you will “see how Dennis Venema answers any objections,” which implies that you will read Dennis’s answers.  You have not committed yourself to reading Durston’s posts and trying to understand them.  And from your dismissive aside about “creationist captain Kirk Durston” the most reasonable inference is that you wouldn’t accept any correction offered by Durston even if you did read his posts.  

I’m sure that Kirk will eventually answer—provided that he hasn’t already covered Dennis’s new question in his previous comments.  Beyond that, all I can say is that Dennis’s latest answer is disappointingly brief, given the care, rigor, and detail of Kirk’s previous reply.  But perhaps, if you and I get out of the way, both of them will get into full swing again.  Neither one of us is contributing to the scientific arguments anyway.


Dennis Venema - #74190

November 6th 2012

Hi Jon,

Sorry for the wait - we’ve had a stomach flu working its way through our (young) family for the last week. Looks like I’m the latest victim. I’ll get back to this when I am able. Best,

Dennis


Jon Garvey - #74193

November 6th 2012

Sorry to hear that, Dennis. My bass player has had it for a week as well - must have crossed the Atlantic!

Jon


Dennis Venema - #74236

November 8th 2012

So, life is slowly getting back to normal, though I’m still not 100%. 

In re-reading this, it still seems to me that Kirk is calculating a probability of a protien coming into existence all at once. I’m not sure how he squares that with the presence of orthologous, but non-coding sequences in non-human primates. Kirk, I’m not sure if you accept shared ancestry for humans and other life, but it’s relevant to the discussion - perhaps you could clarfiy?


Jon Garvey - #74258

November 9th 2012

Here’s a lay perspective: the scenario in question seems to be a gene sequence developing by neutral mutation free from selection in human ancestors, ie essentially randomly. True? Finally one or more statistically quite probable mutations occur, and hey presto! A new functional gene.

If the process had been a one-off assembly, the probability is akin to digging a random hole on an island and finding, first time, a hoard of 200 doubloons. Probability is 1:4^[length of gene sequence]

But if I’ve described  the initial scenario right, the 200 doubloons are scattered across the island, making a higher probability of finding treasure each time , but our digger in 200 random digs has struck gold every time, and kept the coins in his sack, and so got the complete hoard in 200 goes. (This ignores DNA sequence, but I’m assuming a coin as equivalent to the right base in the right order). Kirk seems to be saying that the probability is no higher than the previous scenario, which is intuitively obvious, and indeed that it’s actually lower (which is beyond my maths ability, but doesn’t alter that qualitative conclusion that it’s pretty damn unlikely).

One reason the odds could be worse than the all-at-once scenario is that there’s every chance of the genetic sequence mutating in the wrong direction at any stage during its pre-functional history - the equivalent of a hole in the treasure digger’s sack.

The only way, it seems to me, of reducing the odds is by the old Darwinian gradualist dictum that every change confers a selective advantage - but that’s not what’s being described.


Dennis Venema - #74280

November 9th 2012

Hi Jon,

I’m not sure I fully understand your thoughts - might just be my flu-addled state (seems this flu hasn’t given up on me yet). 

There are many, many sequences in genomes that are close to becoming an open reading frame (i.e. coding for a protein). It’s one of the headaches of annotating genomes, since there are things that look similar to genes that aren’t. The examples from the Wu paper that Kirk and I are discussing are human proteins that have very, very similar sequences in other primates - but in these other organisms these sequences are not proteins. With a large enough genome there will be rare mutation events that make these sorts of non-coding sequences into proteins - that then might come under selection. Presumably we only see the ones that “stick” - i.e. come under selection. 

So, there’s no “need” for these things (since the organism got along fine without them before they showed up) and as such no “need” to find any specific target. These proteins are all quite small and 59 of the sixty have no introns - pretty much what you would expect for proteins that recently arose out of non-coding sequences.  


Dennis Venema - #74281

November 9th 2012

Another point to make is that such proteins (that have no similar protiens in other organisms) cannot be evaluated using the “functional bits / Fits” measure that Kirk sets out in his paper. Fits are determined by comparing related proteins, and determining to what extent amino acids are restricted at a given position in a protein. A protein that has just become an open reading frame from a non-coding sequence (and has no requirement to have any given amino acid at any one of its positions) would have zero functional bits by this measure, as far as I can see. 


Page 1 of 2   1 2 »