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The Yes side on this comes across as trying to elevate important but minor elaborations into major disagreements, seemingly just to raise the status of their work.
Sounds like he/she has spent too long banging their head against group think and is coming across slightly too dramatic. "Science advances one funeral at a time" (although he said physics, taken a liberty there)
That's a pretty cheap ad-hominem attack.
I don't think ad-hominem apply's when the counter argument is:

"The evolutionary phenomena championed by Laland and colleagues are already well integrated into evolutionary biology, where they have long provided useful insights."

AKA, sure what your saying is true, but these are old ideas.

Critiquing an opponent's motivations, as the post I responded to above does, is by definition an ad hominem attack.

The 'No, all is well' article is awash in fallacious rhetorical devices, beginning with an implicit argument from authority and concluding by implying that the EET camp haven't 'paid their dues' yet, as exemplified here: We could stop and argue about whether ‘enough’ attention is being paid to any of these. Or we could roll up our sleeves, get to work, and find out by laying the theoretical foundations and building a solid casebook of empirical studies. Advocacy can take an idea only so far.

The 'Yes, urgently' article depends on increased predictive power of inclusive models, with the various individual examples being signposts on the way to that destination.

> Critiquing an opponent's motivations, as the post I responded to above does, is by definition an ad hominem attack.

No, its not. If the ascribed ill-motivation is used as a basis for dismissing their claims, then it is the ad hominem fallacy. If the claim is rebutted and that rebuttal is used as part of the basis for a critique of potential motivations, or if a critique of potential motivations is used in a context in which it is not the basis for dismissal of the argument, then its not ad hominem.

I'm not seeing any rebuttal in the comment I originally replied to.
I thought for a moment that this comment was intended for the systemd article.
The difficulty is that evolutionary theory is both simple and comprehensive, so almost any extension of it is easy to subsume under the general rubric of the existing consensus. But this is not to say that conceptual modifications aren't potentially interesting.

We see this in physics, where even before the modern revolution we had two completely incompatible, contradictory conceptual approaches to motion: Newtonian mechanics (forces cause motion) and the classical mechanics of Hamilton and Laplace (minimizing the action causes motion). Although these two approaches are mathematically equivalent, they are conceptually entirely different, and only one of them is sufficiently extensible to subsume quantum mechanics (unless you believe Bohm's quantum potential theory, which attempts to explain single-electron atoms as resulting from a new force that holds electrons still.)

We live in an era where we use Newtonian physics as the metaphor for almost all causation. We may be entering an era where Darwinian explanations are similarly dominant, and it's worth thinking about variations on the Darwinian theme to see what kind of mileage we can get out of them. Some may turn out to be surprisingly general and powerful.

My own fictional, speculative look at what might result from an axiomatic, mathematical approach that generalizes Darwinian evolution to, well, pretty much everything, can be found here, if anyone's interested: http://www.amazon.com/Darwins-Theorem-TJ-Radcliffe-ebook/dp/...

In scientific disputes where there are no obvious complaints about unscientific practices or pseudoscience, I simply go with whichever side is less emotionally invested, on the theory that those who are invested have a personal interest at stake. Such a thing is, of course, unlikely to be related to the truth of the matter and that is the point of this.
Historically it's the other way around.

>Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science.

When Discovery Institute successfully brought creationism into the classroom it was able to do so on the grounds that there are holes in the Modern Synthesis. Since then it has become politically incorrect to question the validity of such a claim without walking on eggshells.

Rewrite history much? They brought it into the classroom through politicians. When it went to court it was thrown out as junk science.
"We hold that organisms are constructed in development, not simply ‘programmed’ to develop by genes. Living things do not evolve to fit into pre-existing environments, but co-construct and coevolve with their environments, in the process changing the structure of ecosystems."

I thought that these were already generally accepted ideas within evolutionary theory.

They really are, and I did my biology degree in the 80s and even it didn't really seem controversial. Yet there is a long history of people attempting to make themselves appear iconoclastic.

So look at the Amazon description of this book: http://www.amazon.co.uk/How-The-Leopard-Changed-Spots/dp/075...

I met its author just after it was published. It's a very good book and very interesting, and makes you think about developmental biology in new ways. But even it was always an added nuance and richness to the evolutionary story, rather than the revolution claimed in the blurb.

" For instance, leaf shape changes with soil water and chemistry. SET views this plasticity as merely fine-tuning, or even noise. The EES sees it as a plausible first step in adaptive evolution."

So the EES model believes these organisms are evolving as they grow to adapt to a changing environment. Am I reading this right? Do any organisms actually have the ability to modify their genetic code as they develop?

Gene expressions are not binary. Code may not necessarily need to be modified-- merely activated or deactivated per expression levels. That said, I wouldn't be surprised if code does in fact get 'modified' over time (but there is the problem of separating code from data in your model even then).
> I thought that these were already generally accepted ideas within evolutionary theory.

They are. See e.g. epigenetics and the seminal studies about how grand-maternal environment can affect children.

Agreed. This is not the first such article posted to Hacker News. My take is that there appears to be a subset of evolutionary biologists who, as in far too many fields, are unaware that qualitative research is possible (or not allowed by their departments to practice such), and try to force reality to fit their computer models, to which then there has to be a constant "reaction" to the oversimplification.
So, uh, what James Lovelock has been saying for 40 years, then?
More to the point would have been:

Does popular understanding of evolutionary theory need more depth and nuance?

The concepts of co-evolution and the symbiotic relationship between an organism and its environment are both established and obvious. The growing body of information related to non-genetic inheritance is very interesting, but it's not really a broad "rethink" of the core concept of evolution.

Still, it brings forth a few concepts that don't really get out of the classroom and into the mainstream such as the roles of behavior and teaching on reproductive success. When the subject comes up in the coffee house you'll hear appeals to `intelligence` or `strength` as intrinsic traits. Many successful organisms accumulate advantages through life (e.g. knowledge, immunities, strength). Some of these accumulated traits can be passed to offspring (knowledge through teaching; immunities through mother's milk); others simply aid the individual in achieving greater reproductive success. This isn't new information nor is it surprising to folks with knowledge of the subject, but it is missed in a more secular setting.

Unfortunately, it's hard to get to even this level of nuance because the public hasn't got past "survival of the species" and "nature vs nurture."

The relationship between organisms, ecologies, and the planet needs a more nuanced treatment in the classroom, as well. We didn't evolve on some static geological feature -- we evolved to live in a fetid stew of the waste products of previous generations of life. We are merrily terraforming the planet in our turn, and other lifeforms must now evolve toward success on a planet that has been thoroughly infested with homo sapiens sapiens. Of course, whether we will successfully adapt to the changes we have made is a (rather important) open question.
I agree - also the idea (which you hint at) that life and the environment are not static. The idea that change is bad, is myopic and very human, although very understandable when change involves your environment disappearing.
"organisms are constructed in development, not simply ‘programmed’ to develop by genes"

I really wish people who have no slightest idea about programming STOP using the "programs are inflexible" metaphor.

Programs are the most flexible things known to man.

Genes are not blueprints but they are certainly code.

To be pedantic, life is the most flexible thing known to man.
Life is not known intimately to man yet. We're still in the metaphors phase as you can see.
The concept of a 'program' exists outside computer circles. One easy example is the program for a theatre show. Or a TV channel.

And even within computer programming, a given program is inflexible for most users; only a blessed few are able to alter it, and then only under certain circumstances (access to source code or debugging tools are one of those). Good luck changing the program on your local ATM, for example, even if you are a talented programmer.

Say what you want about the tenets of evolutionary theory, at least it's an ethos.