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Author
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Topic: Macroevolution redefined in terms of evolvability
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gedanken
Member
Member # 594
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posted 06. September 2003 01:53
Woah, Woah, Jack, too sensitive!
In your opening paragraph you ask people to tell their thoughts. And in your last response to me, you ask again for others who are “knowledgeable” to comment on details. I happen to know that Rex is very knowledgeable about biological systems and evolution, so I would think that you were asking for a response.
At first I thought you wanted to set the particular definition for the distinction to be made yourself, but then it became clear that you would let others pick and you wanted to discuss possibilities for such a micro/macro distinction.
I think we were trying to get you to do a couple of things.
One was to separate out your statements or claims about evolution from your statements about which aspect would be suitable for use as a distinction. You could simply state “this is a distinction to consider”. (We can’t argue it is something that could be considered.) Then if you want to make claims about that distinction to support its meaningfulness as a dividing line, those could be considered separately from the issue of whether the distinction forms a crisp or objective and sharp dividing line. You’ve got to realize that some of your claims about evolution were going to be objected to by biologists, and could separate those out so they could be discussed separately (e.g. on page 2).
The other is to discuss whether any proposed measure is a crisp or sharp distinction. For example we could use different definitions of “speciation”. One definition might be used by one camp, and it has one objective test. Another definition might be used by another camp, and it might have a different objective test. The different objective tests might produce different results – and thus there is a degree of arbitrariness in the selection of that test. However in those cases, each of the potential speciation definitions produced a fairly sharp dividing line – just not necessarily a dividing line that everybody would agree was meaningful. We need to distinguish the meaningfulness of a distinction from its crispness or sharpness and its objectivity. It might be sharp and objective, but meaningless – a worthy point for discussion. Or it might be meaningful, but not crisp or sharp or clearly and objectively dividing – different subjects which were getting all mixed together by all of us.
On “polarity” I think Rex was thinking you meant “directionality”. But I think you probably meant it had a digital nature. But consider that many people might find there to be a much greater amount of fuzziness and lack of objectivity in measuring “inventiveness” than in an objective test like ‘can these two organisms mate’. The latter is pretty much subject to a yes/no objective test that can be run in essence in a (possibly outdoor) laboratory. Inventiveness could be argued over with sufficient subjectivity that you could get more opinions than you have individuals in the discussion. So we have a question of whether you were looking for a more crisp dividing line, or were you looking for a dividing line that had a certain type of meaningfulness, even though it might be much more fuzzy and unclear than the original choice of a particular definition of speciation. I think you are the only one who can answer that, and to make sense we needed to have some discussion to bring out the issues.
You did ask. Give it a chance.
[ 06. September 2003, 02:02: Message edited by: gedanken ]
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Jack Foster
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Member # 79
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posted 06. September 2003 22:38
I apologize for not restraining myself. Believe me, . . . I tried.
I guess I'm disappointed that ISCID brainstorms is not a true home for brainstorming. There simply does not appear to be a critical mass of IDists. I think critics are important for bringing any particular brainstorming session back to earth. But if critics are all you have in a brainstorming session, how is the session going to actually explore anything? All ballast and no lift.
I don't think this is the critics' fault, and I apologize for taking my frustration out on them.
Is ID dead?
[ 06. September 2003, 23:09: Message edited by: Jack Foster ]
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Nel
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Member # 614
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posted 06. September 2003 23:21
Speaking for myself, as an ID proponent, I have been spreading myself a bit to thin lately. I should participate more in your threads because they are pretty good. When I get some time (tomorrow) I'll try to participate more in your threads.
[ 06. September 2003, 23:22: Message edited by: Nelson-Alonso ]
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Rex Kerr
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Member # 632
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posted 06. September 2003 23:43
I seem to have a different idea of brainstorming than Jack does. In the biological sciences, it has been my personal experience (and, I would argue, well-demonstrated by history) that almost everything you think about a system is almost entirely wrong, if you are simply going on theory rather than testing experiments.
Brainstorming is normally done in a context of human interactions, which are very forgiving. You can generate 50 ideas for an advertising scheme, and all of them will have substantial merit. In this realm, what is important is that you throw out lots of ideas, and build upon the ones you've already got.
However, when it comes to biological sciences, I find it much more useful to generate ideas and then immediately check to see if they can be tested--because they are probably wrong, and if you can't test them, you won't know. There's little point building an extended theory around something that isn't, at it's core, amenable to testing. Of course, the very first step in brainstorming is just to come up with the idea--but I think the very next step should be to decide whether, in principle, at some point, solid tests could be devised; if the answer is "almost certainly not", then it's time to try another brainstorm.
So while it is true that I am a critic of ID rather than a proponent, I think my apparent role as a critic here (and in most ID threads) is mostly due to wanting to refine the initial idea to a stage where we can see that it could be tested, before elaborating/extending/classical-brainstorming with it.
If I can see a way to make an idea crisp enough to test, I'll propose it. If I can't, I'll gripe that it isn't crisp enough to test. Personally, I think it is hard for good science to be done without someone playing that role.
With respect to "polarity", Gedankin is right about differing interpretations of the word. Perhaps John thinks biological systems are distinctly either inventive or not (what I would call a binary classification), but that may be because he's not aware of certain biological systems.
For example, consider the case of Ephs and Eph receptors (EphRs). These are matched pairs of ligands/receptors that are laid down in various parts of the body, often in opposing gradients, that help neurons find their appropriate partners. (For example, the retinal gangion cells express various EphRs at various levels, which find their appropriate target in the LGN by matching their level of EphR to the matching level of Ephs in the LGN; since each is graded from strong to weak, you get a mapping from the retina onto the LGN.) Pretty handy! This is quite an inventive system; it gives new directions of evolvability since you can, with this system, map different brain regions onto each other more precisely.
Except it's not that simple. There are lots of gradient-based ligand/receptor pairs. Ephs have a certain function, and that allows a wider range of phenotypes, but was it only the original ligand/receptor pair that was inventive, or is Eph an inventive modification of the ligand/receptor idea? Furthermore, there are many subtypes of Ephs and EphRs, and these have some specificity for each other, allowing multiple maps to occur at the same location, or enabling more accurate mapping (presumably--this isn't as well tested). Is that inventive too? Even though it can be reached easily enough by duplication and divergence of existing Ephs (i.e. clearly an evolutionary process where drift and selection are sufficient to generate new Eph/EphR pairs).
Biology is absolutely chock-full of examples like this, where you find many, many systems at every scale between translation of RNA to protein (how's that for inventive!) to overactivating an existing gene that kicks small molecules out of a cell (pretty uninventive drug-resistance!). The key words there are from and to. There are many, many examples at every level in between. So to me it looks very non-binary.
This is, again, why I care about a crisp definition of "inventive": we need to evaluate this huge mess of biological systems, and if most systems are classified as, "Dunno if this is inventive or not!", we won't get very far.
And, this is why I care that the definition be meaningful (i.e. that it reflect a significant actual difference): we could say that everyone 5'9" and taller was "tall", while everyone 5'8" and shorter was "short". But this would be stupid, as I described before. Doing the same thing to biological featues with an arbitrary definition of inventiveness would be equally stupid.
So what we really need is a way to quantify inventiveness, and then we need to use this method to classify various biological structures, and then we need to see if we get clear dividing-lines so that a classification of "inventive" or "not" makes sense. That's my "positive" contribution to the brainstorm: this is what we need to make progress.
Unfortunately, I don't have any idea how one would do this; indeed, I suspect that it is either impossible or difficult enough to be effectively impossible in practice. But, of course, someone else may be able to see how to.
Added in edit: since almost all ideas are mostly wrong, I am also very forgiving when people come up with ideas that are wrong. Just this week, for example, the group I work with decided that one of our models for the role of G-proteins in sensation of noxious chemicals was wrong. The collective reaction was basically just a shrug--yup, it happened again. Importantly, we decided this before trying to publish our ideas. (And I could give you three other examples from people I talked to today.) Anyway, bottom line is: ideas are great, but evaluate them quickly, and if they don't look promising or at least testable, try something else! (At least that's my opinion.)
[ 06. September 2003, 23:55: Message edited by: Rex Kerr ]
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Mike Gene
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Member # 149
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posted 06. September 2003 23:48
Jack,
Like Nelson, I’m spread too thin. Right now, I’m focused on the eukaryotic flagellum and I envision at least two more essays concerning this topic. But I do enjoy reading your postings!
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Nel
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Member # 614
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posted 25. September 2003 14:44
Hi Jack,
Great post. I was interested in something you said here, and wanted to share some thoughts from Keller's articles:
quote:
Evolvability does not evolve in man-made evolutionary systems; it exists at some fixed level as a quality of the system. Biological evolution is different because of the ability of biological evolvability to evolve. This is why macro-evolution has been difficult to demonstrate via "dry" systems.
I think however, that engineers are beginning to raise their eyebrows at the great advantage of evolvability. Computer programmers have begun to develop what they call software for reliable networks:
quote:
"During the past two decades, programmers have attacked the dependability problem by developing fault-tolerant software-programs that allow computer systems to restore normal operation even when problems occur. The technique eliminates the chains of internal dependencies that link the operation of a system as a whole to the operation of any single component. The resulting systems do not need to shut down even if some sites go off-line. Instead they resume service by rapidly reconfiguring to work around crashed servers.
source
Another area where this is comming through is the demand for faster and cheaper power in computer systems. One of the ideas in the field is to build molecular logic devices. These systems rely on self-assembly and self ordering of the system components.
Perhaps the most explicit example where evolvability in biological systems informs engineering is amorphous computing. Gerald Jay Sussman is spearheading this:
quote:
"Computer Science is in deep trouble. Structured design is a failure. Systems, as currently engineered, are brittle and fragile. They cannot be easily adapted to new situations. Small changes in requirements entail large changes in the structure and configuration. Small errors in the programs that prescribe the behavior of the system can lead to large errors in the desired behavior. Indeed, current computational systems are unreasonably dependent on the correctness of the implementation, and they cannot be easily modified to account for errors in the design, errors in the specifications, or the inevitable evolution of the requirements for which the design was commissioned. (Just imagine what happens if you cut a random wire in your computer!) This problem is structural. This is not a complexity problem. It will not be solved by some form of modularity. We need new ideas. We need a new set of engineering principles that can be applied to effectively build flexible, robust, evolvable, and efficient systems.
source
Where do we look for the solution? Biology:
quote:
From biology we learn that multiple strategies may be implemented in a single organism to achieve a greater collective effectiveness than any single approach. For example, cells maintain multiple metabolic pathways for the synthesis of essential metabolites or for the support of essential processes. For example, both aerobic and anaerobic pathways are maintained for the extraction of energy from sugar. The same cell may use either pathway, or both, depending on the availability of oxygen in its environment.
ibid
ID predicts that the line between fields such as computer science and Biology will become ambiguous. Already it is becoming difficult to know which is serving as a metaphor for the other, or even to distinguish our descriptions of one system from those of the other. For example, Hartwell et. al. say things like
quote:
A number of the design principles of biological systems are familiar to engineers. Positive feedback loops can drive rapid transitions between two different stable states of a system, and negative feedback loops can maintain an output parameter within a narrow range, despite widely fluctuating input. Coincidence detection systems require two or more events to occur simultaneously in order to activate an output. Amplifiers are built to minimize noise relative to signal, for instance by choosing appropriate time constants for the circuits. Parallel circuits (fail-safe systems) allow an electronic device to survive failures in one of the circuits.
Designs such as these are common in biology.
source
a convergence of design, that is all too familiar to computer scientists and engineers who work with positive and negative feedback, parallel circuitry, fail safe systems, etc.
Of course, the problem is that these systems are actually designed by external intelligent agents. But the systems in nature exist to a much greater degree of sophistication, such that it informs these external intelligent agents today. Thus it may be crucial to define macroevolution in this respect, because the question becomes, if intelligent agents did not design the systems in nature, then how did these systems evolve?
[ 24. February 2006, 02:29: Message edited by: Nel ]
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Rex Kerr
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Member # 632
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posted 25. September 2003 22:02
If ID predicts that the line between biology and computer science will become ambiguous, doesn't it predict that we will intentionally design computer systems with the flexibility and fault-tolerance of biology, using our intelligence?
Computer scientists revert to evolutionary algorithms when they can't figure out how to solve the problem "intelligently".
Surely ID doesn't imply that an intelligent designer didn't know how to design things, and thus when faced with challenging problems, let evolution create the necessary systems?
Remove the designer, and that's just what Darwinian evolution would say.
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Nel
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Member # 614
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posted 26. September 2003 10:58
Rex writes:
quote:
Surely ID doesn't imply that an intelligent designer didn't know how to design things, and thus when faced with challenging problems, let evolution create the necessary systems?
I wasn't talking about evolutionary algorithms. I was talking about how intelligent designers would mimic the complex mechanisms of evolvability. The complex mechanisms themselves are seems to be very sophisticated technology. As James Bailey states:
quote:
growing indications that in many cases either single genes do not affect phenotype, or that their influence on phenotype does not arise in a simple, obvious fashion.
Bailey, JE, Lessons from metabolic engineering for functional
genomics and drug discovery, Nature Biotechnology, 17:616–618, 1999
[ 26. September 2003, 10:59: Message edited by: Nelson-Alonso ]
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Brad Herp McFall
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Member # 930
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posted 21. October 2003 17:48
Gedanken's link suggested that creationists have an ONTOLOGICAL sense absolutely invoked when discussing any potential, actual, or absolute difference of "micro" and "macro" evolution. I think however that as to ontology it is the evolutionist Lerner who sought in his description of "genetic homeostasis to ONTOLOGICALLY ground MESOEVOLUTION - a term introduced by Dobshansky perhaps indeed after the aboutcom dating of a prior use of the words. In any event it seems to me that the sense intended by Goldschimdt and hence Gould as to "proper scaling into geological time" there IS an EPISTEMOLGICAL instantiation instead. Should our way TO KNOW this seperation exist THEN the ontological issue whehter for creation or evolution could be attached but indeed it does seem to be the suggestion that macroevolution is epistemologically different than microevolution. Indeed, Marston Bates wrote in 1950,p232 "The Evolution of Major Organic Types Richard (who lives in California) has maintained stoutly, in the face of almost universal disagreement from other biologists, that there are two very different kinds of evolution, micro-evolution and macro-evolution." I would love to see this difference resolved first and only in terms of MESO"evolution" but the duality in the field leans more to the fatherest possible splitting of views until the truth shines thru.
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