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Ch. 8: Biology is Engineering 
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 Ch. 8: Biology is Engineering
Ch. 8: Biology is Engineering


Please use this thread to discuss the above listed chapter of "Darwin's Dangerous Idea: Evolution and the Meanings of Life" by Daniel Dennett.



Thu Feb 16, 2017 11:49 pm
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Post Re: Ch. 8: Biology is Engineering
I haven't given up on the book, but maybe I have on this discussion. It's very difficult to understand some of the concepts laid out in this book, let alone try to discuss them intelligently. But here's something from Ch. 8, the "Evolution Is Engineering" chapter that I'll toss out there. Dennett discusses the necessary interaction between evolution and environment, using the example of a seagull's wing that if taken to aliens elsewhere in the universe would show the kind of atmosphere that was necessary for those wings to evolve. He also talks about the the way proteins take on a very specific 3-dimensional shape in the presence of a certain sequence of amino acids. He therefore puts forth a case for agency without skyhooks if that makes any sense:

Quote:
Through the microscope of molecular biology, we get to witness the birth of agency, in the first macromolecules that have enough complexity to “do things.” This is not florid agency—echt intentional action, with the representation of reasons, deliberation, reflection, and conscious decision—but it is the only possible ground from which the seeds of intentional action could grow. There is something alien and vaguely repellent about the quasi-agency we discover at this level—all that purposive hustle and bustle, and yet there’s nobody home. The molecular machines perform their amazing stunts, obviously exquisitely designed, and just as obviously none the wiser about what they are doing. . . . Love it or hate it, phenomena like this exhibit the heart of the power of the Darwinian idea. An impersonal, unreflective, robotic, mindless little scrap of molecular machinery is the ultimate basis of all the agency, and hence meaning, and hence consciousness, in the universe.


I read an article in the New York Times that shows an actual video of a one-celled microorganism using a kind of harpoon to target and capture its prey, which I believe is another kind of dinoflagellates. Is this agency at work? It's one thing chasing after and catching another. Pretty cool video.

https://www.nytimes.com/2017/03/31/scie ... .html?_r=0


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Post Re: Ch. 8: Biology is Engineering
geo wrote:
I haven't given up on the book, but maybe I have on this discussion. It's very difficult to understand some of the concepts laid out in this book, let alone try to discuss them intelligently.


I agree completely. I'm appreciating the bits of new and interesting ideas as I struggle with the readings in Part 1 and 2, but I just don't have enough background information to contribute intelligently to a discussion on the subject, although I did find this chapter 8 one of the more interesting ones.
I have just finished reading chapter 12 of Part 3, "Mind, Meaning, Mathematics, and Morality". Having more background info in this area I'm getting much more from this section of the book. I may contribute something later.



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Post Re: Ch. 8: Biology is Engineering
Good to know the discussion isn't dead yet! I wonder if it's unfair of me to say that the author might assume that everything fascinating to him will also fascinate the reader. Maybe his audience is really those few who have the deep background to go along with him. I do give him a lot of credit for tackling scientific issues with his philosophy background. No doubt, considering the length of the book, there are some nuggets that even we could find worthwhile to talk about. The challenge is to find them and bring them out.



Mon Apr 24, 2017 7:44 am
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Post Re: Ch. 8: Biology is Engineering
Did you guys check out that NYTimes link? It's a perfect illustration of the idea that biology is engineering.


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Post Re: Ch. 8: Biology is Engineering
"There's only so many ways to build a harpoon gun" says the scientist. This is one of the points Dennett likes to make about evolution, that even absent links of descent, there are similarities between animals and plants that are best explained as the emergence of the solutions that succeeded across a number of environments.

That really is a remarkable piece of video.



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Post Re: Ch. 8: Biology is Engineering
DWill wrote:
"There's only so many ways to build a harpoon gun" says the scientist. This is one of the points Dennett likes to make about evolution, that even absent links of descent, there are similarities between animals and plants that are best explained as the emergence of the solutions that succeeded across a number of environments.

There are a couple of points I want to underline from Ch. 8. The first is that, until we get to "communicating organizations" (which includes, by the way, internal communication within an individual) all global order must be generated by local rules. That tells us a little about "order" and a lot about "communication." I think it is a very valuable principle.

So, Dennett is saying that "engineering" went on, and goes on, as a process of solving "local" problems such as eating, healing, warding off predators and parasites, and reproducing. And the rules which set limits on those processes are going to exert heavy influence on the design process. In the extreme, everything is a product of adaptation, and repetitively found solutions (such as the umpteen different types of eye) represent evidence of those rules (constraints, we economists call them.)

Consider for a moment what that tells us about communication. The ability to describe, conceptualize and respond to elements of reality ("there's a lot of rich food over to the NNW", or "if you hang from branches that small, one of them is going to break some day") opens up entire new possibilities for adapting. At the low end, we have signals, like what ants and bees use. At the higher end, we begin to see the possibility of changing the engineering process itself, so that, for example, the constraint on walking and running imposed by the toughness limits of feet can be solved by inventing shoes.

This works, as Dennett's principle points out, by imposing overall order: by seeing how the parts relate to the whole, and thus seeing how a part can be modified, perhaps in some previously unknown way, to allow it to modify the overall problem of the whole. Relation of means to ends is known as "strategy", and we have essentially no evidence of any animal except the great apes creating strategy: maybe some tool creation by elephants, parrots, dogs and dolphins.

Reflection on the ends themselves, in a sort of "meta-strategizing," is the characteristic of "spirit". It has dramatic implications for AI. We imagine that AI's will serve our purposes, with some kind of strange absence of master-slave dialectic which we ought to give some thought to. But at some point, I think not too distant, they won't. When they are rich enough to choose strategies of their own devising (rather than a choice set delimited by our programming), they will be able to decide if they "like" those strategies and change their goals.

The second thing I want to underline is "von Baer's laws" of embryology. The course of "ontogeny" (the development of the embryo) is set by highly conserved controls on the DNA for embryology. Dennett follows Kauffman in concluding that this conservation is seen because we just don't see the mistakes: an error in deriving, say, relation of ribs to spine, will probably make the whole project fail. When we consider the high ratio of miscarriages to births (probably between 1/3 and 1/2 - it is difficult to tell about early blastocyst development) it is possible that they are right and the same ratio of errors to correct copies occurs in the early stages of the process.

But I follow "traditional Darwinian theory" in suspecting that the replication of DNA is much less fiercely controlled in later "decision points" within the development of the organism. This in turn would imply there is some sort of "locking in", such as redundant error-checking, which can happen to replication, but that nature uses it sparingly.

Finally, just because I don't think others will raise it, I want to register my impatience with Dennett's interest in semantic wars such as over whether nature "tinkers" or not, and even whether the design principles resulting from nature's constraints are "laws" [(rolling eyes dramatically)]. Evidently he likes a good metaphor as much as the next person, to help think about how complex processes work, but for some reason some metaphors suddenly reveal themselves to be monsters disguised as natural creatures, and he must slay these dragons before they burn the whole countryside. If he would lay out clearly what he thinks they represent and why he thinks they are inaccurate (better still, what he would replace them with) I would not find such discussions so irritating. But he prefers the impression of a casual stroll, with him as tour guide pointing out which mushrooms are poisonous, with perhaps a bit of elucidation on what part of the body they damage.

DWill wrote:
That really is a remarkable piece of video.
It is. It starts to make some of the mechanisms of, say, viral replication, look very realistic, rather than dauntingly complex. And it still presents an interesting challenge for those who want to work out what "local" mechanisms may have gotten the overall mechanism off the ground, and how they worked helpfully without giving the result of the final product.



Sat Jun 24, 2017 9:07 am
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Post Re: Ch. 8: Biology is Engineering
geo wrote:
Quote:
Through the microscope of molecular biology, we get to witness the birth of agency, in the first macromolecules that have enough complexity to “do things.” This is not florid agency—echt intentional action, with the representation of reasons, deliberation, reflection, and conscious decision—but it is the only possible ground from which the seeds of intentional action could grow. There is something alien and vaguely repellent about the quasi-agency we discover at this level—all that purposive hustle and bustle, and yet there’s nobody home.

Nicely put, I think. "Nobody home." Which raises the question what kind of communication process, representing reasons and enabling their evaluation, means that "someone is home."

Not for nothing did religion create an "age of accountability".



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Sat Jun 24, 2017 9:11 am
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Post Re: Ch. 8: Biology is Engineering
Harry Marks wrote:
Nicely put, I think. "Nobody home." Which raises the question what kind of communication process, representing reasons and enabling their evaluation, means that "someone is home."

Not for nothing did religion create an "age of accountability".

Hi Harry, good to see you still batting these ideas around. Please explain what you mean by an "age of accountability".

I see one of the purposes of religion (and literature and art for that matter) as trying to make sense of the sometimes warring factions of our brains—the so-called "duality" that has been discussed by philosophers for ages. Descartes postulated the existence of a non-physical mind (consciousness), and Freud coined the terms: Id, Ego and Superego to describe our psyche. Robert Louis Stevenson fictionalizes our conflicted mind in his novel, The Strange Case of Dr. Jeckyll and Mr. Hyde.

In biological terms, you can try to imagine an intellect built on top of the primitive underwiring to understand why we are such conflicted beings. Our modern philosophers have to look at our evolutionary heritage to make sense of our brains, but it is this basic idea—the intellect built on top of the primitive brain—that helps me think about how humans operate.

This morning I happened to come across this video of an antelope escaping from a crocodile. What causes the first antelope to be spooked? And what causes the second to stay? But, more to the point, when the crocodile attacks, the antelope reacts purely from the part of the primitive brain (precisely, the amygdala) that deals with danger and fight-or-flight response. Humans have that primitive instinct too, but we also have evolved a larger brain that gives us some measure of autonomy and the ability to reason through our decisions. It's not hard to see that the moral and intellectual parts are sometimes in conflict with our more primitive impulses.

https://www.youtube.com/watch?v=ErohHoOGgyU

Sorry to be so incommunicado lately. We have had a crazy couple of months. We bought a fixer upper in a nearby town so that we can sell our old house. It has been a very expensive ordeal, moving and packing up books and all that. I had put my copy of Dennett's book in a box to go to our new house, but forgot to bring it with me on vacation. I haven't seen my Kindle for a while either, but I reckon it will turn up.


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Post Re: Ch. 8: Biology is Engineering
geo wrote:
Harry Marks wrote:
Not for nothing did religion create an "age of accountability".
Please explain what you mean by an "age of accountability".
Both Roman Catholicism and much of Protestantism have the practical idea that below a certain age a child is not "damned" by their "sin." It's a complex idea to try to explain, but roughly the idea is that a child, up to a certain age (I have heard as young as six and as old as nine), does not reflect on his or her behavior with an internalized idea of responsibility and guilt. You can "get caught" and "get in trouble" but the idea that you are "doing wrong" is still abstract and not something that matters to the choosing process.

Since a soul has the possibility of modifying itself (that is from Kierkegaard, not traditional catechism) it doesn't make sense to hold a child accountable for whom they choose to be, before they are old enough to take "doing right" on board as their own project, not the project of outside people. I am pretty sure some kids are more rebellious and some are more compliant pretty early on, but that part of their personality has not become a character in the internal drama over which side is to be deliberately chosen, until a certain kind of self-awareness becomes part of the process. I think seven or eight is a good guess as to when that usually happens.

Does that mean "nobody is home" in Dennett's usage, before that age? Not exactly, in a mental sense. Plenty of five year olds can play a decent game of chess, for example, complete with imagining what the other player is likely to do. In my view there really is such a thing as spiritual latency before the brain is mature enough to reflect on its own choices.

geo wrote:
I see one of the purposes of religion (and literature and art for that matter) as trying to make sense of the sometimes warring factions of our brains—the so-called "duality" that has been discussed by philosophers for ages. Descartes postulated the existence of a non-physical mind (consciousness), and Freud coined the terms: Id, Ego and Superego to describe our psyche. Robert Louis Stevenson fictionalizes our conflicted mind in his novel, The Strange Case of Dr. Jeckyll and Mr. Hyde.
Well, all of that is the idea. It helps if we don't try to conceptualize the entire process as internal. The Superego (to the extent that such a thing exists) clearly comes from the strange association between complete dependence on parents and the parental role in educating us as to the rules and moral requirements of living in society. The Transactional Analysis people have documented the tendency to "playact" (unconsciously) when we take a "Parent" role in transactions with others, such as admonishing a co-worker or expressing disgust over the way "some people" behave. The Parent is inside us, and we "act like" that parent. As a result, the Superego is a social process as much as it is an internal element of the mind struggling for dominance.

Anyone who thinks degree of rebellion or compliance is determined mainly genetically should talk to some Japanese or Koreans who have lived in a foreign country and tried to return home and fit in.

geo wrote:
In biological terms, you can try to imagine an intellect built on top of the primitive underwiring to understand why we are such conflicted beings. Our modern philosophers have to look at our evolutionary heritage to make sense of our brains, but it is this basic idea—the intellect built on top of the primitive brain—that helps me think about how humans operate.

Humans have that primitive instinct too, but we also have evolved a larger brain that gives us some measure of autonomy and the ability to reason through our decisions. It's not hard to see that the moral and intellectual parts are sometimes in conflict with our more primitive impulses.

I think the best, and richest, approach to dealing with this is in the "Emotional Intelligence" framework popularized by Daniel Goleman. Because it treats the intellectual process as naturally integrated with the emotional processes, and allows for skills of interpretation, empathy and self-calming to play a role in devising strategies and thus increasing skills, it is more open to the dynamics of the natural process than, say, a Freudian model derived mainly from the dynamics of neurotic behavior.

Haidt is also very good - his model of an "elephant" of unconscious moral judgment ridden (mainly helplessly) by an intellectual "explainer" is oversimplified, but it captures important aspects of the truth of moral processes.

"Planet Money" had a good episode on how easy it was to get people to help out with a fraud by framing it for them as helping a colleague escape from (undeserved) trouble, rather than getting themselves rich. I think most people don't reflect much on moral issues, and therefore are unprepared for the ethical dilemmas when they happen. This leaves the elephant in control, or, to put it another way, this leaves them very open to manipulation.
geo wrote:
We have had a crazy couple of months. We bought a fixer upper in a nearby town so that we can sell our old house. It has been a very expensive ordeal, moving and packing up books and all that.

Sorry to hear about the hassle. Good luck finishing with the move, and I hope the Kindle gets found without much trouble. I hate being separated from mine.



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