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Author Topic:   Non-circular Definition of Homology/Analogy
Doddy
Member (Idle past 4250 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 1 of 12 (399377)
05-05-2007 10:08 AM


In discussing (read: debating) evolution with one of my classmates, I used homologous structures as an example/proof of evolution. I know it's not the best argument, but I think it can work.

Anyway, the problem was that both of us were a little rusty in the nomenclature of evolutionary biology, and he didn't remember what homology was, and I couldn't give an explanation that didn't assume evolution to be true (which I know is often pointed out by creationists, as it's on the EvoWiki claims page).

So, I ask, what is a good definition of homology and analogy?

I propose this:

Analogy: similarity between two organisms that is due to adaptation to perform a function
Homology: similarity between two organisms that is not due to adaptation to perform a function

So, for example, the shape of the wings of a penguin are similar to the flippers of a seal, as both have adapted to perform the same function, so can be called analogous. But, the bones in the wings of a penguin are still similar to that of other birds, for no functional reason, indicating homology.

I think I accurately prevented circularity in my argument here. I seem to be using adaptation, which is pretty similar to evolution, so I worry I may not have the best wording. If I put the word 'design' in there instead, it doesn't change it much, so I think it's pretty good. I'm aiming for it to address the idea of God reusing designs when there was no functional need to do so.

However, I fear these example aren't as precise as they could be. And also, I'm not sure whether a structure could be considered both analogous and homologous to the same structure. I don't know whether they are usually, but my definitions don't seem to allow it.

So, do you agree with my definitions? If not, can you help me fine-tune these definitions, in any aspects?

(Evolution section would be a good place, but it could also fit in the ID section I guess)


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AdminNosy
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Message 2 of 12 (399405)
05-05-2007 11:46 AM


Thread moved here from the Proposed New Topics forum.

  
JustinC
Member (Idle past 3185 days)
Posts: 624
From: Pittsburgh, PA, USA
Joined: 07-21-2003


Message 3 of 12 (399586)
05-06-2007 8:02 PM


Well, I'd say homology would best be defined as:

quote:

Significant similarity between two structures of two different species in which no functional explanation can suffice to explain.

Basically, you have all these similarities in structure that have no explanation (pentadactyl limbs of tetrapods, for example). If you assume they were independently created, then the explanation is that the similarities is due to the whim of the creator, i.e, not much of an explanation at all.

If you assume common ancestry, then these type of similarities are to be expected since form is constrained by descent from a common ancestor. So common ancestry predicts these type of non-functional similarities.

I think this argument is not the best one to use off the bat since it requires a little bit of meditation on the subject before the "Ohh..I get it!" moment comes about.


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Doddy
Member (Idle past 4250 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 4 of 12 (399590)
05-06-2007 8:39 PM
Reply to: Message 3 by JustinC
05-06-2007 8:02 PM


That's a good definition Justin. Personally, I would have put 'adaptation' instead of 'explanation'. On the other hand, that might not be the wisest thing...

I think this argument is not the best one to use off the bat since it requires a little bit of meditation on the subject before the "Ohh..I get it!" moment comes about.

The guy I was talking to is a biochemistry student. He, like me, has also done a first year subject on evolutionary biology. I'm confident he will do some meditation on it.


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Brad McFall
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Posts: 3428
From: Ithaca,NY, USA
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Message 5 of 12 (399648)
05-07-2007 7:35 AM
Reply to: Message 3 by JustinC
05-06-2007 8:02 PM


quote:
If you assume they were independently created, then the explanation is that the similarities is due to the whim of the creator, i.e, not much of an explanation at all.

Yea, it is not much of an explanation if the lack of functionality is only in the mind of GOD but indeed there is an extension in a creationist's mind on this topic, at least there can be.

The "product" of evolution implicates that the similiarity in form that possesses no function might. This is why in the evolutionary context Gould named "exaptation" but I do not know of any comparable defintion for an IDist. This seems thinkable to me.

Anyway there IS some burden on the evolutionist because Darwin did use the word "product" and this must be systematically unthought in a structure of evolutionary theory unless some aspect of a design be admitted regardless of any progression in believed in creationist circles.

Edited by Brad McFall, : end of sentence


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JustinC
Member (Idle past 3185 days)
Posts: 624
From: Pittsburgh, PA, USA
Joined: 07-21-2003


Message 6 of 12 (399735)
05-07-2007 5:23 PM
Reply to: Message 5 by Brad McFall
05-07-2007 7:35 AM


quote:
The "product" of evolution implicates that the similiarity in form that possesses no function might. This is why in the evolutionary context Gould named "exaptation" but I do not know of any comparable defintion for an IDist. This seems thinkable to me.


Maybe you can reword this a little better, I think I get the gist of what you are saying but I'm not entirely sure.

I believe some creationists argue that there really aren't such a thing as homologies as I've defined them: all the similarities are there because of functional contraints. For example, during development mammals develop pharangeal arches that seem to be homologous with a fish embryo's pharangeal arches. But, the pharangeal arch stage is essential for the development of individuals in both species as part of their "somatic program" so this would be considered a functional constraint.

The burden is on the evolutionist, in this case, to show that it could have been different. But this case hardly applies to every case of homology. For instance, humans can be born with six fingers and function just fine in the world. This case might also come in criticism since I think that the mutation for six fingers, when homozygous, is lethal. So the creationist would say, again, that the five fingers are the result of a functional constraint.

But to avoid all this we can just look at the amino acid sequences of organism's proteins. It is known for certain several spots in a functional protein's amino acid sequence can be substituted by another without any major deleterious effect on the protein's activity. Similarity in these spots are clearly homologous due to common ancestry (or the whim of the creator).


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Brad McFall
Member (Idle past 3374 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 7 of 12 (399754)
05-07-2007 6:59 PM
Reply to: Message 6 by JustinC
05-07-2007 5:23 PM


exaptation vs aptation with respect to "homology"
This is only a minor point, not like the one I was making with Spasms nor what Mioism may think is less than a whole but one I am sure you can get.

The word “product” is not one that an evolutionist would use (like we may recognize that “purpose” or “progress” are not ones either) but it can be found in Darwin’s work “product of evolution”( I can retrieve it from Goulds work). It is not meant that organisms are products like lawn mowers or hats but if ID were true it would be important for a creationist to explain what aspect of biological change creates what kinds of “products”. I can imagine a USE of evolutionary theory where we may (by artificially selecting natural selection groups) get some suchresults (this is what I intended under the term “ecosystem engineering” http://aexion.org/ecosystemengineering.aspx ) but with the generation of some such productions the flesh of this generation would include some kind of “design” made as far as the ductility of evolutionary theory permits . This is the kind of thing lacking in current expositions of ID and creationism as far as I see it.

One would be in a precarious position as vis a via the/a definition of homology if such a state of ecological research were to develop ( thus I am not saying that creationism has this documentability to its credit nor in it’s “hopper” even if I might). While researching a response to Spasms I came across a creationist distinction that would imply that an exaptation would need be designed by creationists in this instance where one may speak of nonessential functionality later made functional by “creation science” of these ‘products’ but it would be obvious that an organ that was similar without function(al explanation) that later becomes artificially selected for and exists is still the same “homologous” organ no matter the artificiality in the selection. There may even be genetic issues that prevent such products from being designed but/and I had not taken this analysis beyond a simple phenotypic devolution.

I hope I have not made my couple of senetences more confusing. This idea is a little bit more involved than a creationist one where they may claim, as you noted, homologies are controlled by functional constraints wholly. I would suggest that that is too narrow a perspective for the creationist who thinks thus. In either case, the creationist who discusses as you noticed

quote:
For example, during development mammals develop pharangeal arches that seem to be homologous with a fish embryo's pharangeal arches. But, the pharangeal arch stage is essential for the development of individuals in both species as part of their "somatic program" so this would be considered a functional constraint.

or my own demands that the genetic base of this “somatic” program be detailed. The onus in that case would be on both of us. By calling it a “program” this other creationist would have already decided that there was a latent functionality already missed by the evolutionist while in my scenario I would say that the designer, man, creates the function (in a different sense than exaptation) that was not there before (aptation vs exaptation evolutionarily ( I am not sure Gould got aptation correct but this is taking the dissection a bit further from the creationist slant I am presenting here
Defintions and Levels of Analysis(html)

http://tbeauchaine.psych.washington.edu/papers/definitions.pdf
)

I am in agreement with all in you last two paragraphs. I just thought that the “neutral” region was a bit larger than you wrote of. That is all. That is why I thought that a creationist would have an even larger issue in their brains than the evolutionist (this is why for instance Beauchaine in the pdf above can wonder why Gould had not defined the term expatation biologically first and foremost (Gould’s use of the word “feature” has never worked fully for me))if scientific creationism could create “homologies” that they had thought were “independently created by God”. Now they would find that the independence was a function of their own thought not Gods’.


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mick
Member (Idle past 3327 days)
Posts: 913
Joined: 02-17-2005


Message 8 of 12 (399787)
05-08-2007 3:26 AM
Reply to: Message 1 by Doddy
05-05-2007 10:08 AM


doddy writes:

he didn't remember what homology was, and I couldn't give an explanation that didn't assume evolution to be true

Homology describes the existence of similarities between organisms that are the result of descent with modification. As such, homology is generally a hypothesis, which when supported, provides evidence for evolution.

If one rejects the notion that species arise through descent with modification, there is by definition no such thing as homology, there is merely similarity. Creationists are completely wrong-headed if they argue that "homology is best explained by the creator using similar designs for similar functions" or something along those lines. From my definition of homology above, it is clear that these kinds of arguments make no sense. What they really ought to be arguing is that "there is no such thing as homology. What you think is homology is merely similarity".

How might we go about testing the hypothesis of homology? The way I look at it is that there are similarities between organisms, whether one accepts evolution or not. Take the genetic code, for example. There is no arguing about the fact that the genetic code is remarkably similar across all organisms, yet some differences exist (with a vertebrate code, several invertebrate codes, etc).

Evolutionary theory successfully predicts the distribution of these similarities across different life forms. For example, it is a straightforward prediction of evolutionary theory that the genetic code of a mouse and rat will be more similar than the genetic code of a mouse and a nematode, because rat and mouse share a common ancestor more recently than rodent and nematode.

The distribution of similarity across species provides evidence that homology is a real thing in nature. Not just one protein, but all proteins, all physiological functions, all behaviours and all developmental processes are more similar between rat and mouse than they are between rat and nematode. The hypothesis that this vast array of similarities exists by virtue of being the result of descent with modification is then simply the most parsimonious explanation of the observed data.

Creationists have to argue that these patterns essentially mean nothing, that the observed data arose through an unidentified mechanism which simulates homology without really being homology. It doesn't take much thought to find such a viewpoint unsatisfactory. It neither explains nor predicts anything. As such, the distribution of similarity between organisms appears to reflect homology, and is predictable on the basis of phylogenetics, which is strong evidence for the reality of the evolutionary process.

Until some creationist ventures to explain the repeated correlation found between phylogeny, form and function, it seems wise to accept the reality of homology.

Mick


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JustinC
Member (Idle past 3185 days)
Posts: 624
From: Pittsburgh, PA, USA
Joined: 07-21-2003


Message 9 of 12 (399883)
05-08-2007 5:09 PM
Reply to: Message 8 by mick
05-08-2007 3:26 AM


quote:

Evolutionary theory successfully predicts the distribution of these similarities across different life forms. For example, it is a straightforward prediction of evolutionary theory that the genetic code of a mouse and rat will be more similar than the genetic code of a mouse and a nematode, because rat and mouse share a common ancestor more recently than rodent and nematode.


How do you establish that a mouse and rat share a common ancestor more recently than either with a nematode? Here you are assuming common ancestry and hence your argument is backwards. You are saying that since a mouse and rat share a more recent common ancestor then they will share more homologies, but what you should say is that since they share more homologies this is evidence that they share a more recent common ancestor.

Now, after you establish common ancestry through the comparison of several homologies you may make the prediction that more homologies will be found. But you can't forget what got you to establish more recent common ancestry in the first place: homologies.
[EDIT]
I may be misreading your argument here. It sounds like you assumed they had a common ancestor to begin with but I think that you may just be saying you assume this by virtue of it being your hypothesis.

quote:

The distribution of similarity across species provides evidence that homology is a real thing in nature. Not just one protein, but all proteins, all physiological functions, all behaviours and all developmental processes are more similar between rat and mouse than they are between rat and nematode. The hypothesis that this vast array of similarities exists by virtue of being the result of descent with modification is then simply the most parsimonious explanation of the observed data.


I would also quibble with this a bit. It's not the distribution of similarity that is evidence of evolution: it is the distribution of homologous (non-functional) similarities. Of course a mouse and a rat are going to share a lot of similarities in terms of anatomy, physiology, and behavior than if either one is compared to a nematode. This is because they have relatively similar niche.

It's the non-functional similarities that are interesting.

Edited by JustinC, : No reason given.

Edited by JustinC, : No reason given.

Edited by JustinC, : ambiguity


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Wounded King
Member (Idle past 2436 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 10 of 12 (399977)
05-09-2007 1:01 PM
Reply to: Message 9 by JustinC
05-08-2007 5:09 PM


I would also quibble with this a bit. It's not the distribution of similarity that is evidence of evolution: it is the distribution of homologous (non-functional) similarities. Of course a mouse and a rat are going to share a lot of similarities in terms of anatomy, physiology, and behavior than if either one is compared to a nematode. This is because they have relatively similar niche.

It's the non-functional similarities that are interesting.

I can see where you are coming from here but I really don't think you can just dismiss anything functional, not to mention that fact that many IDists or creationists will dismiss the idea that there is anything non-functional to look at in the first place, see the many arguments based on vestigial organs for a reminder of this.

A whale and a mouse have quite distinct niches but they still share several clear and functional similarities which are a viable basis for considering them both placental mammals and would lead you to consider a marsupial mouse the outsider on the basis of such features. There are also a number of morphological feature on which we might come to the contrary conclusion, but the more features we look at and the more species we add to our analysis the more apparent it will be that there are more shared features between the placental mammals than marsupials, especially when we bring genetic data into the analysis.

None of this requires any prior assumption of homology, simply the systematic organisation of the organisms on the basis of similarities. Such comparisons will shoe up examples of both homology where gourps of similarity cluster together and convergent or analogous similarities which occur in disparate groups.

Maybe you are just using non-functional in an unusual way in terms of morphological features, it seems highly biased toward the sort of molecular comparisons you mentioned earlier, if not then your view seems pretty restrictive.

It isn't as if the lack of a clear slam dunk argument for every homologous structures against a creationist ploy should be the basis for the scientific definition of a term. When I discussed the pharyngeal arches with Randman he continually moved the goalposts back, the deeper the morphological, molecular and genetic homologies got the more evidence he required. There is no point ignoring perfectly good scientific evidence in favour of exactly the right flavour of evidence to convince those who are not open to conviction.

TTFN,

WK


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JustinC
Member (Idle past 3185 days)
Posts: 624
From: Pittsburgh, PA, USA
Joined: 07-21-2003


Message 11 of 12 (400009)
05-09-2007 5:32 PM
Reply to: Message 10 by Wounded King
05-09-2007 1:01 PM


quote:

It isn't as if the lack of a clear slam dunk argument for every homologous structures against a creationist ploy should be the basis for the scientific definition of a term.


I accept your criticism and recognize that I'm using non-functional in a highly restrictive manner. When writing I was tacitly responding to the plethora of creationist critiques against using certain (seemingly homologous) features to infer common ancestry. That is, every so-called homology is a necessary functional constraint.

For example, that fact that baleen whales develop teeth in the embryo just like toothed whales seems to me good evidence of common ancestry. But a staunch creationist would reply that the tooth whaled stage is necessary for the development of baleen and is therefore a necessity, yadda yadda yadda. I know the counter-argumnent is extremely frivilous and vacuous (especially considering their claim that creatures were created by an omnipotent being: why use the same developmental pathway?)

So you are correct, the term used in science shouldn't be as restrictive as I proposed.


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Doddy
Member (Idle past 4250 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 12 of 12 (400154)
05-10-2007 7:37 PM
Reply to: Message 11 by JustinC
05-09-2007 5:32 PM


JustinC writes:

especially considering their claim that creatures were created by an omnipotent being: why use the same developmental pathway?

I wonder that as well. One of the explanations given by AiG for why ratites have wings and related structures (such as a broad sternum) was "design economy":

http://www.answersingenesis.org/docs/446.asp

quote:
It is a result of ‘design economy’ by the Creator. Humans use this with automobiles, for example. All models might have mounting points for air conditioning, power steering, etc. although not all have them. Likewise, all models tend to use the same wiring harness, although not all features are necessarily implemented in any one model. In using the same embryological blueprint for all birds, all birds will have wings.

Why an omnipotent being, to whom nothing can be difficult, would need to take shortcuts is beyond me.


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