The Minimal Genome Project: "Here we report a new cell"

[Nuno]

Hi @Eddie,

I agree with your reading of Behe’s views - the sentences following the excerpt I sent continue to extend his position in that direction. But the main point I was making, and that Behe and you also make to some extent, is that irreducible complexity is different from whether a system of parts can emerge by natural processes. In brief, to say that a system S is irreducibly complex just means that if you remove any of its parts then it will cease to perform its typical function. This, of course, does not preclude that a system T with 95% of the same parts could have existed with a different (though probably somewhat similar) function and that T could thus have been the precursor from which S emerged with a lot less need for novelty than if S just emerged out of nowhere in just one step.

I would also not be exceedingly surprised if new mechanisms of genomic evolution were discovered - it was not so long ago that the importance of RNA and epigenetics was seriously underestimated so I don’t think you’ll find many people defending that we’re definitely done defining how genomes can evolve. As such, a formal proof could likely be easily constructed showing that nucleotide polymorphisms are not enough to generate the diversity of life we see today - even a single reversal or crossover can already generate way more variation than would be probabilistically reasonable with just polymorphism rates within a single generation. But this only proves that certain mechanisms are not enough - it does not establish the impossibility that other mechanisms (e.g., duplications, etc.) cannot help things move faster and eventually bridge the “evolutionary rate gaps” that we observe today.

Denton’s hypothesis is an interesting twist on the ID conversation - isn’t it somewhat contradictory to argue on the one hand that a) only intervention by an external intelligent being can bridge gaps in evolution or abiogenesis (e.g., Meyer) and on the other hand argue that b) the laws of nature are so predetermined that the outcomes we see today are all nearly inevitable (Denton)? How are these views reconciled within the ID realm?

[gbrooks9 (George Brooks)]

@Eddie

What I like about the ID community is its intellectual breadth; because every view of origins (OEC, YEC, and evolutionary) can be found within it (except hardcore, materialistic atheism), an ID proponent is always kept on his intellectual toes by his own allies. Behe has to listen to OECs like Meyer and YECs like Nelson; Nelson and Meyer have to listen to evolutionists like Denton, etc. Even though I accept common descent, I don’t mind periodically hearing criticism of common descent from intelligent YEC-ID folks; it’s good for people not to become intellectually complacent, and to review every now and then the things they take for granted and without critical examination.

What @Eddie is describing is the full range of all the different beliefs that are humanly possible when one believes in God. I would agree that this is the glory of any world view that includes the participation of a divine mind.

It’s one thing to say, like I do, that BioLogos is a part of that God-centered spectrum. But it’s an error to write “… [two-way movement] would not be possible within the TE/EC community.” Because it is not the 2-way movement that is not possible… it is. What is different is what the benchmarks would be.

Right here on the BioLogos boards we have people who support millions of years of Evolution - - but only through God manipulating environments… not manipulating genetics directly. Then we have folks like me who think God can shoot a DNA sequence with a Cosmic Ray at 10 billion light years and 10 paces.

And there are those who think God would ONLY intervene in evolution with LAWFUL events, while others think he would ALSO intervene with actions that are NON-LAWFUL from the viewpoint of science.

[Nuno]

@Eddie

@Eddie

Neo-Darwinian evolution, in its classical form, is essentially “blind search rewarded or corrected by natural selection.” But it may well be that we will discover that much evolutionary change does not proceed by blind search. That is why I find the ideas of people like Shapiro and Wagner (ideas running in different directions, to be sure, but both differing from notions of blind search) promising.

As I’m sure you will appreciate, I find it important to clarify what exactly is meant by “Neo-Darwinism” and “blind search”. Both Shapiro and Wagner make use of mechanisms like horizontal gene transfer (both) and symbiosis (more Shapiro, though this is commonly accepted biology too) but it is not clear why you would exclude these mechanisms from your definition of “blind search”. Even though these mechanisms differ from simple mutations of genomic sequences between generations, their occurrences are still modeled as stochastic events that generate new genomic diversity to be filtered by natural selection. Maybe you meant an expanded definition akin to “blind search [in offspring genomes derived solely by modification of parent genomes] rewarded or corrected by natural selection”?

Note that even accelerated genomic responses to environmental changes such as the adaptive immune system are, in a sense, “blind search” generation of diversity followed by “natural selection” of response to a stimulus. And as long as such adaptive responses to stimuli are not shown to be heritable then we would still be in the realm of non-Lamarckian inheritance. That said, somatic mutations in the progenitor reproductive system can be heritable so it is possible that if foreign genomic sequences were to become inscribed in reproductive cells then these could also eventually become fixed in the human genome. However, this would likely also be a stochastic process so it should remain within the realm of “blind search”.

It would seem that proper alternatives to the definition of “blind search” evolution should include at least some level of teleology. That would be the fundamental distinction between ID models and “blind search” evolutionary models - the former claims that the parts are precisely arranged to serve a specific purpose while the latter only claims that the aggregation of the parts survives because it served a purpose.

@Eddie

Such two-way movement is possible within the ID community; it would not be possible within the TE/EC community. I like that freedom from the pressures of “consensus.”

I have not followed the history of TE/EC/BioLogos close enough to have encountered flagrant examples of “pressure towards consensus” but I can imagine that there could be a tendency to be conservative, at least to the levels of the mainstream scientific views. At a time when Christianity is struggling to counter the public perceptions developed in response to the likes of YEC propaganda, it is important to be on scientific grounds that are as solid as they can be. So while I understand your desire to boldly embrace more daring initiatives (such as the upcoming series on divine action/interfaces) as a part of its core theology, it is probably more prudent to keep those in the realm of brainstorm/dialogue while focusing on the core mission of carving the proper middle ground between the extremes of YEC and Dawkins.

[Chris_Falter]

Hi Eddie -

I hope your weekend went well! I bought flowers for my wife, the mother of my children, then I got really adventurous and cooked a meal for her and my Mom.

And we do live in an age of miracles: the family somehow survived.

@Eddie

Read what I wrote: “The “random mutations” of neo-Darwinism were not inspired by quantum theory or chaos theory.”

I read this. However, I was not concerned with it, and never addressed it in my argument. I only included your statement about inspiration in order to give context to the very next sentence, which I also quoted in the same block:

@Eddie

A different sense of “random” was meant.

This is the statement I disagree with. My reasoning is straightforward: if the same stochastic mathematics apply to two different domains, scientists would not think that a fundamentally different sense of randomness applies. Same stochastic math, same stochastic sense.

@Eddie

You are not reading for context.

I heartily agree on the need for reading for context. I would include in this important task the discernment of any subtext in an author’s position. In doing so, we should be gracious and avoid attributing malice, laziness, ignorance, or other deadly sins. At the same time, if an author seems to be doing everything in his power to lead his readers to a particular conclusion, it would be remiss (in my opinion) not to take his/her intention seriously.

I think the heart of our disagreement over Behe boils down to our stance on subtext. You have been urging that only Behe’s actual statements should be attributed to him; anything more inappropriately “reads into” Behe. I disagree. If I’m in a military aircraft, and an officer puts a parachute on my back, leads me to an open door, and tells me the plane is going to crash in 5 minutes, then he means for me to jump. Likewise, when Behe says that the only viable explanation for complex biochemical structures is…

• an intelligent agent
• that acts extremely rapidly
• and has the ability to craft staggering numbers of not-switched-on genetic instructions that direct the construction of highly complex biochemical mechanisms

…then he means for me to ascribe powers to the intelligent agent that are not within the natural realm. That would be the case even in a panspermia scenario, because the question of “who/what made the alien biochemists” cannot scientifically regress to a point earlier than the Big Bang.

I suspect that we are going to agree to disagree on the appropriateness (or not) of dealing with Behe’s subtext (or lack thereof, some might argue). No harm, no foul.

If you would like to take the last word, feel free. Like I said, I have learned a lot from our discussion.

[Chris_Falter]

@Eddie

But for those interested in an alternative line of persuasion for evolutionary creation (defending evolution against mechanical Biblical literalism, but with the emphasis far more on maintaining traditional theological doctrine than on adjusting traditional doctrine to fit in with consensus science), the website called Hump of the Camel provides a model.

Hi Eddie,

Thanks for pointing to this interesting site. I glanced at a couple articles and discussion threads, and found some nuggets of real gold. I will subscribe to the site, and catch up on some of the previous posts. Here is a link for anyone interested in the site.

@Eddie

I would suggest a slight reversal of priorities; instead of spending 80% of its effort at trying to convince conservative opponents of evolution that evolution is established by irrefutable science and has to be accepted (with whatever implications that may have for Biblical exegesis and theology), and only 20% of its effort articulating a historically and theologically sound Protestant evangelical faith, the EC leaders should expend more like 75% of their communicative energy on establishing their loyalty and solidarity with traditional Protestant evangelical doctrine and only about 25% of their energy on the strictly biological arguments.

I’m in the “all of the above” camp: I think we need some groups that adopt the approach you suggest, and some that adopt the BioLogos approach. After all, those of us who believe strongly in the “2 books” of Scripture and nature have a message that can profit many different groups within our society.

Cheers,
Chris Falter

[GJDS]

Hi Chris,

I am glad to hear that miracles (even in our cooking) still occur in this day and age (but we can always have a fall back position from those “burger” places )

While I agree with you in that stochastic means just that for scientists, I want to point out an important difference when we discuss the notions of stochastic and random within the bio-sciences. I can illustrate my point by using a much simpler example. If we take a handful of molecular units and consider the molecular structures, and various conformers for specific structures, that these can provide, we can use stochastic methods to compute all possible molecules - the number would be very large even for 5-6 units (the units may be aromatic, carbonyl, aliphatic, sulfur). We can then compute the ground states of these structures and eliminate those with an unrealistic value, but we are left with a large number. How would we decide which of the remaining structures is the correct one? It would be difficult to arrive at an answer using only stochastic methods, but for restricted cases such as the example I have give, it is possible to provide plausible structure and these can undergo further examination - this difficulty is greater by orders of magnitude when we consider bio-molecules, because these are dynamical systems, and the energies (differences) between various conformers would be small (hydrogen bonding, differing 3D arrangements, just to mention two sources of variation). Add to these the impact of external factors (e.g. uv light, excited states, often radicals) and we have a system that is impossible to understand using stochastic techniques.

It is within this context that proponents of “random” put forward their view on changes that drive evolution. If their claim is taken seriously, science cannot account for the formation of relevant bio-molecules. I am far more charitable in my criticism, by pointing out that even if relevant bio-molecules were “miraculously cooked up” (pun intended) the possibilities that we would need to contemplate as variations in the subsequent dynamical systems would defy our scientific understanding.

I end my musings by pointing out that competent bio-scientists have gone to a lot of trouble to provide numbers to variations in bio-spaces, and their results are numbers that are truly astronomical. Thus when the term “random” is used within the context of evolution, we are way, way, outside the notions scientists associate with stochastic methods.

[Chris_Falter]

Thanks for your helpful perspective and example, George.

[Nuno]

Hi @Eddie,

Thank you for taking the time even on a time crunch. I can certainly relate!

This concept of “blind search” is key to clarifying our views on the claim of evolutionary models so it would be useful to address it in more detail, even if within the constraints of the limited time that is available to devote to these matters. I agree that a definition of “blind search” should include the “random mutations” in classical neo-Darwinism since those mutations are expected to happen in a manner that is not dependent on any particular future endpoint. As such, the example you gave of ducking an object is indeed not a “blind search” since that movement is teleological - the decision to move in a particular direction is based on the explicit desire to avoid the object thrown at me.

@Eddie

I would not call changes in a genome brought on in an attempt to cope with environmental stress “blind” changes, in the sense that “random mutations” in classical neo-Darwinism are blind changes.

Let’s consider this with a specific example, such as a cellular organism C being exposed to heat stress. This change in conditions creates a series of problems (harder to maintain structural integrity, process nutrients, etc) but C doesn’t really “know” or have any pressure to change in any specific direction. That said, one of C’s offspring (e.g., O) can very well gain a random mutation that increases the resistance to heat, in which case we would expect that the offspring of O would thrive while the offspring of C without the mutation would be at a disadvantage and could eventually be out-competed to extinction.

Now while the fixation of the mutation in O was not random, the process of genomic change by which it emerged still was “blind” and “random” in that the relative probability of occurrence of the mutation was not dependent on the endpoint effect that resulted in increased heat resistance. So yes, you would be correct in stating that the evolution of O was not random (in that not all possible outcomes were equally likely) but its emergence was still a result of a “blind search” in the fitness space defined by the environmental heat shock.

This is also essentially what you stated with

@Eddie

classical neo-Darwinism is a blind search, because the mutations that occur are explicitly said to be utterly unrelated to selective advantage

which is correct, even though the fixation of selected mutations is often a very “non-blind” process.

@Eddie

whereas in the suggestions of Shapiro and the differing suggestions of the structuralists, it is not an inherent part of the theory that the genomic changes bear no relationship to selective advantage.

If you could send some information on which sections of Shapiro’s book are perceived to claim that the occurrence (not the selection/fixation) of genomic changes are or could be related to the selective advantage then I would certainly be glad to follow up on that.

There are other points that would also be interesting to discuss with respect to the mechanisms of genomic variation behind Shapiro’s and Wagner’s models but the more fundamental question of whether responding to environmental stress uses “blind search” or not is probably best addressed with just a simple example like the one above.

@Eddie

As for the strategy of BioLogos, that is another subject altogether.

I agree. And since it is not related to the main topic of this thread, I would only mention that I agree with your assessment that it is important for conservative audiences to trust BioLogos as a Christian organization and would only add that it would be great to see the staff and supporters of BioLogos grow more in the directions that you mention. It is a young and vibrant movement with much room to grow and I hope we’ll see it get there.

[Nuno]

Hi @Eddie,

I completely agree with your assessment. Looking forward to the passages.

[Biosemiosis.org]

Bio: Again CONSTANT misrepresentation.

Jon: If I am misrepresenting you then please let me know how.

Sure. I’ll tell you how you are misrepresenting me. In fact, I’ll give you the whole run down.

The topic of this thread was the fundamental necessity of genetic translation. Every biological organism known to exist (prokaryote or eukaryote, single-celled or multicellular, animal, plant, fungus, or bacteria) requires translation. Every virus requires the translation apparatus of its host in order to evolve. Translation is the physical process that enables the organization of the cell, and is itself the product of a specific organization. It is the very thing that has to be explained. As it turns out, genetic translation is an identifiable semiotic process. This core necessity was proposed indirectly by von Neumann’s work on self-replication (before DNA was even understood). The semiosis in genetic translation was confirmed as we modeled DNA and uncovered the details of the translation apparatus in the late 50’s and early 60’s. And by the end of the 1960’s, it was formally presented (in a scientific conference) that indeed “Life is matter controlled by symbols”.

Nuno participated in the conversation for a while, attacking the argument by offering a counter-example of translation from the RNA world scenario. However, the process of RNA “self-replication” and the process of translation are two entirely dissimilar physical processes. Among other things, one is rate-dependent and reversible, and the other is rate-independent and non-reversible. One is wholly dynamic, and the other is the expression of a medium to control dynamics. RNA template-replication does not achieve translation, and is not physically capable of producing the effects of translation. Those missing effects are specifically what is required to organize the heterogeneous living cell. But when these details began to come into the dialogue, (content deleted by moderator)

Then Dennis showed up and made an opportunistic comment about ID. The flaw in his comment could be easily demonstrated (using nothing more than the settled science of translation, clearly published in every biology textbook on the surface of the planet). And since Behe and irreducible complexity are two of this blog’s favorite punching bags, I challenged him on the concept of IC. I stated that irreducible complexity is wholly vindicated by semiosis inside the cell, (content deleted)

It was at that time that you jumped in to ask a question that cannot reasonably be considered anything other than pure rhetoric. Why must it be rhetoric? Because every rational person alive in the modern world already knows the answer to the question: No person has ever used science to produce a “detailed rigorous account” of how life began – designed or otherwise. Thus the only thing to be gained by asking the question was to try to make something out of the implications of my answer. (content deleted).

Not being able to list the details of how design occurred does nothing to lessen the fact that a universal correlate of intelligence has been empirically detected in biology. In other words, your question was just bad rhetoric and you appeared to be milking it for all you could get. Example: After telling you that I agreed with the content of Behe’s statement, you told me that agreeing with the content wasn’t your question. Instead, you wanted to know if I agreed with his statement. (wha?) You then went on to contradict your earlier statements (in at least two instances) and equivocate. And for all this, you are applauded by the gallery for keeping me in line. Good grief.

(content deleted)

You asked if any validating evidence of my claim about IC had been published in the literature. (content deleted) So I pointed you to my bibliography and timeline, and told you that you might want to “pay particular attention to Pattee, Crick, Barbieri, and Koonin, for technical matters”.

Given the variety of people coming to my site, my judgement is that these authors (as well as some of the others listed on the bibliography) offer visitors good overall access to key issues. In any case, I suggested Pattee first because he is likely the world’s leading technical author on the physics of symbol systems. I suggested Crick because of his obvious connection to the issue, as well as his 1961 paper that experimentally demonstrated the “reading frame” nature of the code. I suggested Barbieri because of his obvious domain experience in semiotics. And I suggested Koonin because he is an authority on OoL issues, who writes very clearly about the general condition of OoL research – specifically about the centrality of the coupled translation apparatus to the origin of life, and the absence of good reasoning to believe that evolution had any role to play in it.

Hence the first paradox of OORT: to attain the minimal complexity required for a biological system to start on the path of biological evolution, a system of a far greater complexity, i.e., a highly evolved one, appears to be required. How such a system could evolve, is a puzzle that defeats conventional evolutionary thinking. – Koonin

The second paradox of OORT pertains to the origin of the translation system from within the RNA world via a Darwinian evolutionary process: until the translation system produces functional proteins, there is no obvious selective advantage to the evolution of any parts of this elaborate (even in its most primitive form) molecular machine. – Koonin

And here’s an obligatory quote just for you Jon (this will require you to read for context)

All this is not to suggest that OORT is a problem of “irreducible complexity” and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally. However, it is clear that OORT is not just the hardest problem in all of evolutionary biology but one that is qualitatively distinct from the rest. For all other problems, the basis of biological evolution, genome replication, is in place but, in the case of OORT, the emergence of this mechanism itself is the explanandum. Thus, it is of interest to consider radically different scenarios for OORT. – Koonin

(content deleted).

Nuno: You have to be kidding me - are you really including Eugene Konin’s multiverse hypothesis in your “supporting evidence”? Do you realize that his response to reviewer #1 flat out denies ID … You truly are either confused or trying way too hard to deflect attention … I truly praise Jonathan Burke for his patience to try to keep you on topic

(content deleted) Koonin’s technical knowledge surrounding the origin of life was the issue, which is specifically the reason I had given for suggesting him. Again, regarding the range of visitors to my site, some think that the issues surrounding the OoL are only seen as truly “hard problems” by ID proponents. Koonin’s paper dispels that belief, even as it replaces evolution with an equally ambiguous cause (the anthropic principle) in order to suggest a pathway around the problems.

So now to answer your question: “If I am misrepresenting you then please let me know how.”

Jon: It’s not rhetoric to ask you how you believe Koonin’s paper supports ID.

Jon: you should be more explicit about how you believe Koonin’s work provides any support for ID.

Jon: When you cite a paper which you claim supports ID

Jon: You seem to be telling Nuno that Koonin’s work provides support for ID

Firstly, I did not say that Koonin’s paper supports ID. I included his paper as one (among others) that could offer you insights into the issues involved. (And to subtlety suggest that Koonin’s paper has to support ID in order to be relevant is a ridiculous idea). Secondly, I did not recommend Koonin’s paper because I was going to read it to you. I suggested it (among others) for you to read because – as I made explicit -- I have no interest in trying to get someone to understand something while they drag their feet in socio-political opposition.

Cheers…

[Biosemiosis.org]

“:content deleted”

How about that.

[Christy (Christy Hemphill)]

@Biosemiosis_org

This is just a reminder that telling other people what their motivations are and making negative insinuations about other people’s intellectual capabilities is a violation of our dialogue guidelines. I edited your post for you to bring it more in line. It still has a ways to go to count as gracious, but I realize we can lose touch with our better selves in a heated discussion. But in the future, I’m going to save myself some time and just delete posts that are disrespectful and antagonistic.

[DennisVenema]

@Eddie

You can write more clearly than John Stuart Mill, Bertrand Russell, David Hume, or George Orwell on this site, and you will still be misread. Your words will be taken to support things you haven’t supported, and to deny things you haven’t designed. That is unfortunately the mindset in these debates. Too many people are convinced that they know what you will argue before you argue it, and therefore adopt the attitude that they don’t have to take your actual words seriously, and can just impute views to you based on rumor and suspicion. There are about half a dozen regulars here who do this constantly.

Unfortunately this seems to be the price of commenting on an open forum. Here at BioLogos we highly value that any and all are welcome to comment.

Eddie, it could be worse you know. All of the above is true for me as well, but it impacts me in real life, not just on a forum where I am an anonymous commenter. I’ve had people try to have me fired, and I’ve been forced out of a church community along with my family. So too for many other Christians who are willing to say they accept evolution as good science.

(Before this turns into a pity-fest, I should also point out that I am often hugely blessed by others because of my work here, so there is a definite upside as well. I am surrounded by supportive colleagues, and our new church situation is a huge blessing to us).

So, why do I do this? Mostly because I want to work myself out of a job. In the future, I hope that BioLogos will be as unnecessary as an organization devoted to the harmonious synthesis of heliocentrsim and orthodox faith. I think we’ll get there; I’m hoping it’s within my lifetime.

[Christy (Christy Hemphill)]

@Eddie

Jonathan Burke the other day accused me of being one of the leading anti-evolutionists on this site.

And if I remember correctly, I deleted it. Gee whiz. Quit your whining about each other and either have a discussion or go play free cell.

[Nuno]

@Biosemiosis.org

@Biosemiosis.org

Nuno participated in the conversation for a while, attacking the argument by offering a counter-example of translation from the RNA world scenario. However, the process of RNA “self-replication” and the process of translation are two entirely dissimilar physical processes. Among other things, one is rate-dependent and reversible, and the other is rate-independent and non-reversible. One is wholly dynamic, and the other is the expression of a medium to control dynamics.

Hey - look at that! This is what I was asking for way back in the conversation but wasn’t provided until just now. Maybe there’s even a probability higher than Koonin’s that the conversation will get back on topic.

@Biosemiosis.org

RNA template-replication does not achieve translation, and is not physically capable of producing the effects of translation.

My point was not that self-replicating molecules (RNA or others) achieve translation - my point was that those types of structures could be the precursors that would eventually construct a translational complex.

@Biosemiosis.org

Those missing effects are specifically what is required to organize the heterogeneous living cell.

I agree that there are missing steps and that is all that anyone can say. Obviously no one has a mechanistic explanation for abiogenesis but no one has a formal proof that it cannot happen either. Is a fully detailed mechanistic proof the only way that would convince you that your theory is not a proof of design?

@Biosemiosis.org

Koonin’s technical knowledge surrounding the origin of life was the issue, which is specifically the reason I had given for suggesting him.

I don’t want to belabor the point around Koonin’s views but it’s useful to note that his paper does not support your views in the way you claim it does. Yes, he states that no one knows how abiogenesis happened (no big news there) but his probability calculation does not give you the support you read into it, as you can see by the very quote that you posted:

@Biosemiosis.org

“even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P<10-1018.”

First, no one here (or in the mainstream scientific literature) is claiming that life started out by pure chance assembly of amino acids and RNA into the translational complexes. That is a straw man argument that leads nowhere.

Second, Koonin’s toy model (he admits to it himself, even in your own quote) aims to make the point that even if the probability was that ridiculously small, the events would still occur in his multiverse model. As such, Koonin has no need to strive for an accurate probability calculation since anything resulting in a higher probability would only (redundantly) support his views.

[Nuno]

@DennisVenema

Thank you for sharing your experiences. It certainly adds perspective to the very minor inconveniences of purely online disagreements. For what is worth, I would add that you are doing a fantastic job at “working yourself out of a job” with all the insightful and, arguably most importantly, highly accessible explanations of complex biological concepts to the Christian community.

Keep up the good work!