The Evolution of Evolution: How our understanding has changed

The focal point of most creation-evolution debates centers on the ability (or not) of random mutation and natural selection to account for life's diversity.  This is understandable because it is still what is emphasized and receives the most attention in introductory biology courses.  

So people on both sides of the debate find it surprising and at odds with what they've learned and perhaps even unbelievable when I say evolutionary biology today recognizes that life's diversity cannot be explained by mutation-selection only, that there is much more in addition to this, and a plurality of mechanisms involved.  

I have then talked about the Extended Evolutionary Synthesis, given examples, and posted links articles like microbiologist James Shapiro's "Nothing in Evolution Makes Sense Except in Light of Genomics.  

Reactions to this range from continued denial/rejection of what I say to possible acceptance on the basis of my word, but still without really understanding why.  At least that's my perception, and I've realized (after recent discussions with @MindWalk and @stephen_33 on this topic) that I need to do a better job connecting the dots for people.  

It is my intent to do that very thing with this new thread: to better connect the dots for people as to how evolutionary biology has evolved beyond the standard Neo-Darwinian view (i.e., the Modern Synthesis) of mutation-selectionism, and most importantly *why*, so that people understand the underlying reasons instead of just taking me at my word.

To this end, I have selected an article (that I don't think I've posted on before) that does an excellent job explaining these changes and how advances (especially in genomics) have revolutionized our understanding of evolutionary biology.  The article is over ten years old but still relevant for the discussion, and methodically goes through the issues in a historical, chronological manner that I think people will find especially helpful (so my plan is to similarly follow this approach with a step-by-step walk through this article).  Here's the article link and abstract:

"Darwinian Evolution in the Light of Genomics" (2009) by Koonin

Abstract-
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

*To start with, I have highlighted three key ideas in the abstract:

(1) Natural selection is only one evolutionary force and not the (quantitatively) dominant one.

(2) The popular conception of evolution as an "increasing [trend in] complexity" is a myth.

(3) The new evidence from genomics indicates that a paradigm shift may be in order (*this article predates and anticipates the Extended Evolutionary Synthesis).

***OK, but why?  For those interested, we will walk through the article and see. 

I feel the gene-centric viewpoint enables adherence to the pure mutation/natural selection viewpoint better.

Of course genetic drift does turn out to be important, but this is merely "adaptation" in a neutral direction (evolution does not care how fitness compares to earlier fitness, it merely cares that fitness is achieved).

I would assert the abstract viewpoint is 100% true.

1. Life contains functional information
2. This functional information is slightly imperfectly replicated
3. The distribution of functional information changes exactly according to the empirical mutations and the empirical fitness (by definition) and statistically according to a statistical model of the mutation process and a statistical model of the fitness of different information in the environment (the idea being to replace the actual unpredictable accidents by an exact statistical description of their random occurrence. This is a loose definition as the notion  of "the best model" is elusive, especially for fitness).

From a gene centric viewpoint the environment includes the co-operation between a gene and the genes it is combined with (or is likely to be combined with, from the model viewpoint) in organisms. It even encompasses horizontal transfer although this may be a particular difficult process to predict and model: if it is a one-off for a gene, there may be no evolutionary heritage to help its success?

Or maybe there is - any thoughts, @tbwp10?

In my usual rather fuzzy manner, I'd like the mention the notion that the adding of random neutral diversity may be really important for increasing the probability of later advantageous mutations. Genetic diversity means more candidates are within range to be generated by mutation and tested by natural selection.

Tracking.

The article begins with some background history on Darwinism and the subsequent Modern Synthesis/NeoDarwinism, and then focuses on how genomics has changed our understanding of the latter.  The article first identifies the core, central propositions of the Modern Synthesis/NeoDarwinism:

Here is a summary table from the article that cuts to the chase on how genomics has changed our understanding of evolution:

Is this suggesting there is a goal in evolution? There isn't a target correct, something lives or dies it doesn't favor one over the other? There is no desire to see something happen in a mindless process.

"Of course genetic drift does turn out to be important, but this is merely "adaptation" in a neutral direction (evolution does not care how fitness compares to earlier fitness, it merely cares that fitness is achieved)."

I'll answer your question with some questions of my own same as before:

Is there a thought process behind genetics, genetic recombination, crossing over, random assortment and segregation, jumping genes, lateral gene transfer, etc., etc., etc. that contribute to genetic variation and that we observe occurring in nature?  Does the natural genetic engineering processes that we observe in cells (and that we learned how to do our own genetic engineering from) occur via mindless mechanisms or guided thought?  Does whole genome duplication, gene transfer between organisms, rearrangements and acquisition and incorporation of new genetic material into genomes that we observe happening in cells occur via 'mindless' mechanisms or does an intelligent designer intervene during each and every step along the way?

It is more than processes at play, seasons in weather can be a process but on-off switches control complex system monitoring results and all activities have more going on when these types of things are run due to instructional controls, coded to occur. Those types of processes don't happen by happenstance, they don't just occur and continue to improve over time. I write code to do complex work, once the code is written I trust the code and from time to time make changes to the code to do new work or make a correction due to something not accounted for.

Which respect to having an intelligent designer who had to set up the universe to support life and then life's processes, watching every step of every process would just be a natural thing.

The point is some random processes are 'accidents' and some are not

Exactly what are you saying here? 

Same thing he has been saying, last six years.

The Evolutionary Process, has evolved.

Modern species have evolved, to evolve.

Genomes these days are more apt, to mutate where it might just do some good.

Restating the theory is not proving anything, Is the mechanism for the alteration of evolutionary change by necessity, and chance? How did the information that drives all of the processes get there in the first place, and by what means did these instructions alter themselves without destroying necessary ongoing operations while doing it while under going evolutionary change?

In answer to your questions, I direct you to this comprehensive review article....again!

"Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process"

Cells have mechanisms for "adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification" 

*Operative word is "study". Genome evolution is not some theoretical idea, but a documented, observable reality that "we can now study" in real time 

"That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification."

I'm not sure what it is you think you are showing us here. Saying it reads and writes, is a big deal, but it isn't anything new. It takes a mind to set up code to read and write, is that what you are suggesting? How did the ability to read and write get there?

That's a question of origins, which you and I already agree is a problem, so if you want to believe an Intelligent Designer created in built evolvability mechanisms so that organisms can naturally evolve, that's fine with me.

I don't see it as a problem, for me, it is simply God started life and it works as design, there are no issues from designer to design scenario. The only ones with the problem are those that want to push a round circle into a square hole, they simply don't fit. It isn't much different than what Newton saw in the planetary orbits, he could see the elegance in them, which could be worked out, but the only way they could get in their orbits was, they were put there.

Philosophiæ Naturalis Principia Mathematica

“This most beautiful system of the sun, planets and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being...

So you accept that evolution is a result of natural mechanisms initially put there by an intelligent designer 

I accept that only designed mechanisms can do the things we see in life, you'd have to define what you mean when you say 'evolution' because even without major changes I could agree with the term depending on how it is used and defined.

See the article link above and take time to read and digest 

Yes, repeating the theory proves it, undirected random variation can do it, making the claim proves it can happen.