Question Submission 5

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Griesemer’s example of the chemoton as a possible look at the first lifelike process in class Thursday raised some interest in me of what role emergentism may be able to play is explanation of biological processes. While the chemoton would have many of the characteristic processes of a living thing, it would seem to only be a controlled chemical reaction and, at best, life-like. If a chemical reaction (or a set of chemical reactions) is not truly life, then how can the origin and development of life be explained? What theories or attempts at explanation have been given by emergentist researchers (in particular, whether and how life is simply more than a sum of chemical reactions)? I believe that biology is a rich field for this type of explanation, especially when regarding the origins of life and the units of evolutionary transition, but perhaps my very limited knowledge of emergence is leading me to look for explanations where it does not apply.

My question comes from Godfrey-Smith's chapter "Reproduction & Individuality." In the discussion of chimeras and mosaics, Godfrey-Smith uses as an example the unusual development of marmosets. He states that marmosets typically give birth to dizygotic twins, whose embryos establish links and exchange cells during development, producing two chimeras (organisms composed of a mix of genotypes). My question is: have there been any theories put forth as to why this type of development evolved? Is it simply to increase the genetic diversity of each organism, a type of higher-level recombination event?

My question arises from Prof. Griesemer’s ‘The Units of Evolutionary Transition’ paper and his lecture last Thursday. The lecture states that an evolutionary transition ‘is the evolution of a new biological organization,’ e.g. the transition to a multi-cellular organism state from a previous level comprised of colonies of independently reproducing cells. Additionally, the paper and lecture make multiple references to ‘replicators,’ which Hull describes as ‘an entity that passes on its structure largely intact in successive replications,’ and ‘interactors,’ which Hull further describes as an entity that interacts as a cohesive whole with its environment in such a way that this interaction causes replication to be differential (p.71 in Griesemer, 2000)’. Relating these terms to evolutionary transitions, take for instance the primitive RNA molecule which is thought to have existed as a sole entity in the early days of ‘life.’ This RNA molecule essentially served as both an interactor – it navigated the environment as a lone entity - and a replicator – it was capable of self-duplication/multiplication. Compare this to complex organisms such as humans, which as sole entities exist to interact with their environment, while their existence is dependent upon their replicating constituents. The question, then, is whether it is plausible to explain evolutionary transitions and the overall progression of evolution in terms of the continual distancing of interactor and replicator roles within an organism?

I happened upon a news story yesterday of Venter's work creating synthetic DNA from "scratch." What caught my eye was a quote from Venter, "This is a philosophical advance as much as a technical advance," and it seemed like Venter was implying that the definitions of evolution/heredity/development may be brought into question sooner rather than later. I understand that building a bacterial DNA sequence base by base but copying it from one found naturally is a far cry from creating "purely new and synthetic life," but my question is this; when we understand more about systems of genes and their interactions at lower levels and are able to "build life" do our definitions of evolution and heredity get turned on their head?

Griesemer briefly mentions process ontologies in "Tracking Organic Processes," writing: "Where, when, and how processes originate; what interactions happen to them along their way; and how they terminate is, in a word, what there is according to process ontologies," and continuing, "Regardless of the metaphysical standing of process ontologies, there is no doubt that scientists do follow processes, that this is an important and central activity in their work, and that they achieve causal understanding as a result of doing it" (277).

My question concerns the metaphysical status of process ontologies, and whether Griesemer's argument might have consequences for our understanding of it. In his lecture during the Friday HST/MCPS colloquium, Griesemer emphasized the role scientific theories play in co-determining the phenomena that constitute the object of scientific research. If it is the case that tracking commitments, focused on understanding processes, best characterize what scientists do, does that then indicate that an ontology of processes, rather than of entities, offers a better basis for those phenomena, either because the phenomena are co-determined by a process-focused theory, or because they have proven susceptible to being understood through a processed-focused theory?

At the end of Chapter 4, Peter Godfrey-Smith concludes that relaxing the concepts of individuality and reproduction will allow one to accept, as reproduction, the cases that challenged the intuitive conception of reproduction, so long as we constrain ourselves to an evolutionary context. But his goal at the beginning seems to be a general "reproductive concept" that is consistent with evolution, rather than a concept that is dependent on the evolutionary context. Is this a genuine distinction, or am I reading to far into the terms?

Further, all we need in the evolutionary context is for the entities that result from a "reproductive-like" process to be subject to natural selection. To me, this fails to get at the heart of reproduction, even if all Godfrey-Smith is after is a concept of reproduction sufficient for evolutionary contexts. Why force the concept of reproduction into evolutionary contexts? Reproduction, generally construed, should be consistent with evolution contexts, or at least we should be able to localize where the general concept will fail. So, I am not claiming that we should not have an account of reproduction in evolutionary contexts. What I am asking is to properly characterize reproduction, even for the purposes of applying it to an evolutionary context, shouldn't "reproduction concepts" avoid "evolutionary concepts" at the risk of begging the question?

In the 'Units of Evolutionary Transition', Prof. Griesemer argues for a model of evolutionary transition that accommodates an integral place for development. This requires that reproduction, which includes a more complex process of replication i.e. material overlap and development, is placed beside the copying mechanism that is assumed for the genetic material, or the replicator. One consequence of this is that the interactor is proposed as a parallel unit of evolution to the replicator whereas Dawkin's considered these interactors as entities (be they a protein coat, single cell or multi-cellular organism) which are mere 'survival machines' whose existence and characteristics are designed by the replicators which reside within. Other than through selective survival and reproduction, which is determined by the characteristics that are genetically imparted, is it possible to say that evolution acts upon a concept like the interactor? Isn't material overlap an extension of the previous generations resources, generated by their replicators, just passing over to the new environment (survival machine) of the next generation?

On Tuesday Professor Griesemer was making the point that Mendel is a developmentalist rather than a geneticist. He made the point that the term 'develop' was used almost sixty times throughout Mendel's paper. Then on Thursday Professor was talking about units of evolutionary transition. In this lecture, Griesemer was saying there was an issue with there being different definitions of some words. So why when it comes to Mendel's discussion of inheritance, does the word 'develop' only have one definition that gives evidence of him being a developmentalist? Could there be an alternative definition of develop, like words in Thursday's lecture, that would show Mendel to be a geneticist? To me, it just seems like the professor is just closing his mind to the side of the issue that he wants to present.

On page 82 of "Reproduction and Individuality" (from Peter Godfrey-Smith's book Darwinian Populations and Natural Selection), he writes, "And the most familiar cases of reproduction to us--human sexual reproduction--feature an obvious role for genetic novelty." However, Godfrey-Smith spends the chapter trying to account for our view of reproduction among all organisms.

It seems to me that our concept of reproduction may be tainted by our own experience. Wouldn't it be easier to start elsewhere if human reproduction is the "novelty"? The previous quote, along with the following one--"Sex tends to make reproduction clear, because the offspring cannot be a mere continuation of both parents"--made me think that perhaps we are trying too hard to base an account of reproduction that fits humanity perfectly. We should take into account that the definition of reproduction that we will end up with will be skewed from having started from the example of human sexual reproduction. Is this not important? Do we even have another option for developing this definition?

This question pertains to PGS's "Reproduction and Individuality".

The most succinct way of putting my question is, can we tell a story of in which an individual organism (however one spells that out) evolves over time? Or does evolution require reproduction?

I am wondering to what extent the concepts of evolution and reproduction are distinct/independent concepts. Does an account of evolution require the concept of reproduction or can it make do with only the concept of growth with genetic change? An example of growth with genetic change are the quaking aspens.

It seems to me (and maybe Nick who I talked to about this) that there are two main ways to go: one - insist that evolution requires reproduction and expand the concept of reproduction to include things like an oak tree 'growing' new limbs as reproduction; two - allow evolution to be independent of reproduction and say that an individual organism can evolve. The dispute between my 'one' and 'two' then seems to be a terminological dispute, since either way can tell the same story in different language.

My question comes from Godfrey-Smith's chapter "Reproduction & Individuality," and mainly stems from his writing on Chimeras and Mosaics (and comes in two parts). He states, "birth produces two genets and two physiological individuals, but the genets are spread across the two physiological individuals...a mixture of genetically different cells."

My first question is: Since Chimeras have two distinctly different groups of cells, Is it possible for offspring of Chimeras to have barely or no genetic relationship to their parents?

And if it is possible for the offspring: Are chimeras a common example of development of new and unique species? If so, Are Chimera's evolutionarily favorable?

My question is derived from the Godrey-Smith reading, "Reproduction & Individuality," and is a question of clarification. When discussing collective entities the question is asked when we should begin to look at reproduction as a higher level process instead of a lower level reproduction of constituents. It then goes on to use buffolo and humans as examples. Is this passage rasing a question on whether we look at reproduction and enchancement as an individual process or a group process? If this is the question being raised wouldn't evolution always have to be specific on the enviroment/settings but be large scale on that population to be determined?

My question has to do with stated problem #1-evolutionary transition from Profesor Griesemer's Thursday lecture. The question was brought up as to whether or not genes involved. While thinking about this, I was reminded of the genetic code and its built in "preparedness" for genetic mutation. For example, CCU,CCG,CCA,and CCC all code for the amino acid Proline which allows for some room for error during translation. If the original strand codes for CCC, but by accident CCA is translated, the amino acid will be not change. To me, this seems like something that evolved, but I am not really sure how to explain it. Can you give the argument for both sides ("genes evolving" vs "genes were just created") as it would relate to this topic?

My question is derived from the Godrey-Smith reading, "Reproduction & Individuality," and is a question of clarification. When discussing collective entities the question is asked when we should begin to look at reproduction as a higher level process instead of a lower level reproduction of constituents. It then goes on to use buffalo and humans as examples. Is this passage raising a question on whether we look at reproduction and enhancement as an individual process or a group process? If this is the question being raised wouldn't evolution always have to be specific on the environment/settings but be large scale on that population to be determined?

The opening quote from Maynard Smith to Griesemer's "The Units of Evolutionary Transition" states that "any attempt to formalize an evolutionary problem mathematically obliges one to make, explicitly or implicitly, assumptions about what are the units of selection..." Has the scientific community still not solidified what units of selection are? I thought predation, disease, climate, and catastrophic events (or 'preference' under artificial selection) were the units of selection. Now I am not sure. Do we only know they exist and still debate on what they are? If this is true, I would presume this is a significant source of the confusion mentioned towards the end of the article regarding the 3 stage process of evolutionary transition. Is the lack of certainty of what the units of selection are the reason we do not know why some transitions appear to 'compress or skip' stages? Could it be the functions of selection that allow these compressions or skips to occur?

I want to further explore the role of material connections in evolution. Prof Griesmer argued that a photocopier is rather different than biological reproduction because there is no material from the parent present in the offspring (copy). I would like to bring up two points; the first in DNA replication this material connection between parent and offspring disappear if we do not look at events that are separate in time (that is, the material connection is only preserved through the first round of DNA replication; however, the DNA produced in the first round transmits part of its material to its offspring thus there is a direct lineage that could be traced. Secondly, and this is the crux of my question, Griesmer argues (in the manuscript) that viruses can be send to have a material connection with their offspring given a number of steps (15 if I recall) in which material is connected ( - 1)virus attaches to the cell; 2)virus interacts with cell membrane; etc....15). If this is the case, could we not argue that the paper being copied has a material connection with the photocopy produced given that we can create a set of successive stages - each of which is connected and influences the next one. Or does the material connection have to involve actual molecules from one step to the next?

My question come from the discussion of last Tuesday when it was discuss that Mendel establish his experiment, his experiment were focus in the development area and not in the genetics as it is well know now. Why people thought of his experiment as a genetic and not as a development? Could it be because the genetic idea fit better with the thought of the time? Could it be that Mendel didn’t see his work as a genesis’s because it was not well know at his time?

My question comes from Prof. Griesemer's paper on the units of evolutionary transition. In the section labeled "Biological multiplication entails development" there is a question being raised on the explination of the "levels" of evolution. Maynard Smith and Szathmáry give their component principles in three catagories: Multiplication, Heredity, and variability. The confusion for me comes in when it is said "If objects of different types have a hereditary difference in their fecundity and/or survival, the population undergoes evolution by natural selection." Is this saying that inherited genes which provide inhereted characteristics are directly tied to natural selection? If this is so, why are there divisions between replicators and interactors? In other words should replicators and interactors be said to go hand in hand because one effects the other.

My question is from Godfrey-Smith's chapter Reproduction and Individuality and has to do with his reply to Griesemer's concern for the 'capacity to develop' as being necessary for reproduction. (I realize that Godfrey-Smith wrote that this topic would be addressed later in the next chapter, but unfortunately that chapter was not posted.) I am curious as to how the his notion of 'capacity' differs from Griesemer's. It seems to be the case that one could argue for the 'capacity to develop' to mean that an organism, through changes in its lifetime, comes to a state of being in which development is possible. Furthermore, this is what Godfrey-Smith is saying occurs (though, for some reason he doesn't think that this is 'capacity'). What does Godfrey-Smith mean by 'capacity' then? And how does his argument against Griesemer flesh out?

I've been thinking a lot about ontological commitments: how they express themselves through action and how those actions can be track and interpreted. I'm very interested in how ontological commitments about species effect conservation efforts. An ontological commitment to the "biological" species concept versus the "ecological" species concept would have tremendous effects on how researchers collect data, how policy is written, how conservation projects are carried out and how success is defined. Which ontological commitment would preserve the highest level of biodiversity, or does the concept of biodiversity itself get altered?

My question comes from the Godfrey-Smith reading, "Reproduction and Individuality." I'd like to bring up the "quaking aspen" tree. According to Mitton and Grant, "What look like hundreds or thousands of distinct trees scattered across many acres will in fact be connected to each other by a common root system, from which they have all grown." The hundreds/thousands of "distinct" trees are actually one big tree. For evolution to occur, changes in genetic composition need to happen, and in the case of the "quaking aspen" which grows from the same root system, not much change in genetic composition must occur if it is still technically the same organism. From the reading, I get the sense that reproduction and evolution are tied together. Towards the end of chapter 4, Godfrey-Smith states, "Reproduction involves the creation of a new entity, and this will be a countable individual." According to Godfrey-Smith, since a new entity needs to be created for reproduction to occur, and because evolution is tied to reproduction, are organisms that don't reproduce a new entity but instead continually add upon themselves by growth able to go through evolutionary changes?

Griesemer argues that the units of selection should be expanded beyond Dawkins’s view which only includes genes. He extends the definition of units of selection to reproducers rather than replicators; defining a reproducer as an entity capable of multiplying and transferring some of its parts onto its offspring. Another important component to Griesemer’s case regards the definition of an evolutionary transition, which are, to quote Maynard Smith and Szathmary, “entities that were capable of independent replication before transition can replicate only as part of a larger whole after it.”

Griesemer’s lecture notes included a table of major evolutionary transitions, which include transitions between species (i.e. primate societies to human societies). The idea of whether selection can occur at the species level or higher remains controversial, but does Griesemer’s argument extends to this type of selection? Or are the units of selection limited to individual organisms and smaller biological components?

Godfrey-Smith's views on the relation between individuality and reproduction in chimeras reminded me of an article I read awhile back on the experimentation stemming from the work of (i believe) Dr. White in Australia decades ago when a goat-sheep chimera hybrid was successfully created by way of embryonic fusion of sheep and goat individuals. The formation of the goat-sheep hybrid (or geep, as as the article refereed to it as) is the result of extensive unnatural interaction by humans. My question is does the engineering of a hybrid by such “unnatural” means present a problem to the definition reproduction as outlined by Godfrey-Smith? This question becomes more intriguing when one imagines a future in which science has become so advanced and knowledgeable that hybridization between two, or more, drastically phylogenetically unrelated organisms, by currently unforeseeable means, is possible.

Griesemer argues that the units of selection should be expanded beyond Dawkins’s view which only includes genes. He extends the definition of units of selection to reproducers rather than replicators; defining a reproducer as an entity capable of multiplying and transferring some of its parts onto its offspring. Another important component to Griesemer’s case regards the definition of an evolutionary transition, which are, to quote Maynard Smith and Szathmary, “entities that were capable of independent replication before transition can replicate only as part of a larger whole after it.”

Griesemer’s lecture notes included a table of major evolutionary transitions, which include transitions between species (i.e. primate societies to human societies). The idea of whether selection can occur at the species level or higher remains controversial, but does Griesemer’s argument extends to this type of selection? Or are the units of selection limited to individual organisms and smaller biological components?

In Griesemer's "Tracking Organic Processes", p. 378-379 presents a schema for what a causal process ought to look like in biology, in spite of existing in a dynamic process. The conclusion drawn is that the same schema can be used for explaining development and heredity:

"Heredity concerns the respect in which A stands in a certain causal relation to B, while development concerns the bringing about of B from A. Both concern the very same causal process, both seek an account of causal process in terms of continuity and constancy or invariance, and both investigate it by tracking
marks that identify it as a causal process."

With the schema on page 378 and the above quote, it appears as though development and heredity are contra-positive "sciences". Perhaps this is too strong of a stance on what Griesemer has been trying to argue in rethinking the dichotomy of development/genetics, but I cannot help but see the similarity (irony?). My question is specifically aimed at why the same causal structure can be utilized (seemingly) so differently while studying almost identical subjects? Does this stem from trying to impose a closed system (controlled environment/experiment) on a more or less open system (dynamic)? Is it safe to assume that more refining of the definitions and controls in experiments will clarify this oddity?

In last Thursday's Lecture, Prof. Griesemer talked about evolved Mechanisms of Development within the context of reproduction.


My question may seem too obvious due to my severe lack of a solid Biology background, but I am oblivious to what exactly these mechanisms of development actually are...


Also, I feel as though Prof. Griesemer's definition of a reproducer ended up being very circular. I say this because I understood it as: a reproducer is an entity that transfers some of its parts to new entities, and that some of these parts are developmental mechanisms that carry the capacity to reproduce.

Also sorry I posted this so late, I was traveling this weekend and could not connect to the internet in the airport today.

shawx198 asked:
Since Chimeras have two distinctly different groups of cells, Is it possible for offspring of Chimeras to have barely or no genetic relationship to their parents?

I had a similar question, particularly since the answer seems to bear on the questions of the units of selection, and how we identify individuals. Applying some of the tools we've been given so far, here's what I think:

Griesemer's definition of reproduction requires a material transmission from the parent that confers upon the offspring the capacity to develop through to reproductive maturity. Using the Marmoset example, we will have two fertilization events, M1 and M2, which then exchange cells, giving us chimeric offspring M1,2 and M2,1. If we assume that the chimeric offspring themselves reproduce using only their original germ line—i.e. by reproducing as though they were merely M1 and M2—then it seems, on Griesemer's definition, that chimerism is nothing more than an ancillary developmental oddity, considering the exchanged cells had nothing to do with the offspring developing the capacity to reproduce. In that case we would also diminished difficulty distinguishing between genetic and phenotypic individuals, considering that in Marmoset M1,2 only the M1 component is relevant for reproductive, and therefore for selective purposes.

If, however, M1,2 could reproduce as though it were M2 things get more complicated. I don't think it offers too much of a challenge to Griesemer's conception of reproduction: the parents' genetic material is still the stuff conferring the developmental capacity to attain reproductive capabilities, even though it involves an intermediary and a chance exists that no actual stuff from the parents is carried over on the traveller cells, so we might have to think of the siblings as parents of each other—the situation is weird anyway, though, so that isn't too damning a commitment. It would muddle the individuality issue, though, particularly if M2,1 is capable of reproducing EITHER as M1 OR as M2. For someone like Dawkins, in such a case, we really have two individuals because we have two genotypes. In that case, if we want to avoid a hard reductionist view that it's all just genes, we have to be committed* to something like making the question of how we identify individuals level/domain specific: it will have different answers on the genetic and phenotypic levels, for instance. This view also commits us to a range of positions on the units of evolution/levels of selection debates, considering we've accepted an autonomy of levels for the purposes of identifying the things on which selection acts.

Sorry for writing a novel... I gave a long response because I didn't have time to write a short one.

* Assuming we don't take Prof. Waters' route and say that we're happy for our definition to be a heuristic with a broad, but admittedly limited domain, in which case the exception might prove the rule.

I think your comment this week was interesting, partly due to my shared interest in the topic you discussed but furthermore due to the way you understood the connection between building life and the definitions of heredity and development.
The way I see it, we (Venter's Lab) would not be making these types of advancements in "SYNTHETIC LIFE" if the scientists in Lab were viewing heredity and development within the context of say, a definition that provides a limiting force on new advancements. What I mean is in order to actually execute such an experiment in lab, firstly would require that the scientists involved already have a new conception of what exactly is going on or how exactly things are working in the subject matter.
To put it simply, I think it has to be the case that in doing something they deem never before done, the people involved have accepted a new range of possibilities. These expanded possibilities are intrinsically going to demand a change in the way ideas like heredity and development are understood, in the new broader range of what is possible.

Chris Perdoni asks, "The question, then, is whether it is plausible to explain evolutionary transitions and the overall progression of evolution in terms of the continual distancing of interactor and replicator roles within an organism?"

I found this question particularly thought-provoking since it seems to be getting at the heart of explanations (especially in the context of evolutionary transitions). It also bears on the role certain concepts play in explanations. To answer the question, I think the continual distancing of replicator from interactor is (when we are at a particular transition point where those terms can appropriately apply) a result of evolutionary transition, rather than an explanation of it. That is, what is the explanatory work being done by saying that an evolutionary transition is the distancing of replicator and interactor? Here, I leave open whether it is a good way to qualitatively describe the phenomenon, but I do not believe it would be a good way to explain the phenomenon.

Further, I should clarify the parenthetical note above "when we are at a particular transition point where those terms can appropriately apply" because it bears heavily on my rejection of the explanatory power of the distancing process. Even if we can tease out some explanatory power from the continual distancing of replicator and interactor, we run into problems at the higher levels of organization. What about the population level? In that context, is it appropriate to call the individual organisms "replicators" and the population an "interactor?" Aren't both the individual organisms and the population independently susceptible to evolutionary pressure? Thus, at this level, would we commit to saying that the organism is both an interactor and replicator? Moreover, how do we maintain that it is a replicator in the truest sense that Hull requires? If the organism is both an interactor and replicator, we do not have a distancing process at this level. Then, on your account, do we have a genuine level of biological organization at the population level? Notice, I drop the last qualification of your definition "within an organism" to give you as much power to deal with this level. I leave open whether you can do this or not. At the very least, I think these are at least some of the relevant questions that would need to be answered.

Side-note: I would not say that the human interactor is dependent on their replicating constituents. Rather, the replicating constituents are now dependent on their interactor.

Synthetic biology is the most fascinating emerging biotechnology today, in my opinion. Synthetic biology interconnects geneticists, engineers, and programmers in a way that new life forms will be created with specific functions in mind. The actual behavior of the organism could be modified and engineered genetically to perform new tasks. I believe most definitely that this area of biotechnology will change, and hopefully enhance, our understanding of the connections between genetics and development much sooner than anticipated. The goal is to redesign the developmental process of organisms! I think as genetic engineering and synthetic biology both continue to alter the genetic make-up of organisms, evolution will be called into question as well. Instead of the creation of new species via natural methods, we can simply make one from scratch.

One of my favorite explanations of synthetic biology comes from a New York Times article. The founder of the International Genetically Engineered Machine Competition (iGEM), Drew Endy, spoke about how synthetic biology could shift from needing to chop down a tree, cut the wood into specified dimensions, sand it, and nail the pieces in place in order to make a bookshelf. Endy states, “Or you could program the DNA in the tree so that it grows into a bookshelf” (Mooallem 2010).

Amazing.


Mooallem, Jon. 2010. Do-it-yourself genetic engineering. The New York Times. Available at: http://www.nytimes.com/2010/02/14/magazine/14Biology-t.html

This is a very interesting question. As science is advancing, and we are now able to create synthetic DNA, does this change our view of evolution? In my opinion, this does not change the organic biological changes that occurred during the process of evolution, but if we do start incorporating synthetic DNA into our environment, how will it effect future species development?

It seems to me that intervention in animal reproduction, such as the example of the sheep/goat hybrid, could be seen as simply an extension of artificial selection. Artificial selection leads to reproduction between animals who would have not, in a "natural" setting, have bred. Creation of hybrids by artificial means is basically the same idea. Therefore, I don't think it would be a problem for Godfrey-Smith's view of reproduction.

It is interesting to think about what currents of evolution are dominating contemporary life on this planet. Obviously, biological-based natural selection was the dominate form of evolution for billions of years, then in the last couple thousand years artificial selection became the driving force for the expansion of humanity. Theorists like Kurzweil point out that in the last couple hundred years the evolution of tools have now easily outpaced the evolution of biology. This isn't to say that biological evolution – natural or artificially selected – has stopped (obviously), but that there are parallel streams of evolution that effect the nature of a species more than the much slower progression of biological evolution. Is synthetic biology going to be the next dominate current in evolution? Tools have allowed us to largely circumvent the pressure placed by the environment on our genotype/phenotype by creating environments that are designed perfectly for our survival. Will synthetic biology circumvent the other component of evolution, random mutation? Why wait around to randomly mutate when you can engineer? I'm very skeptical about notions like the 'Singularity', but if we combine the surging evolution of tools with an ability to have a designer aesthetic regarding our genome, it makes it seem like an intriguing (disturbing?) possibility.

I think the picture that Professor Griesemer showed of the quaking aspen shows that they have gone through evolutionary changes because the groups of trees are of different colors. Also, there are so many of the "trees" that they had to have of evolved to make it through natural selection. They would not be around if they have not evolved to maintain in their environment. A gene mutation may occur in the underground root system that causes the trees to evolve and wind pollination could lead to a new series of these trees growing. This shows that a new entity has formed and thus evolution has occurred.

I believe that Griesemer in particular would agree that basing an account not using human reproduction would be vital to understanding reproduction and evolution. I think that this is one of the primary reasons for Griesemer using retroviruses to prove his point on material overlap: he wants to show that his account is not merely an explanation that handles the specific case of human reproduction well, but the extremely different case of viruses, too.

I think it could also be asked, though, whether human reproduction (and other more complex cases) must be reconciled with viral reproduction given their extreme difference. Perhaps starting with human reproduction is acceptable if the account can be universalized, but it may also be the case that different types of reproduction fall under classes that cannot be reconciled in a single base definition. So it then becomes interesting to explore why these different classes of reproduction occur in an evolutionary context, if they do at all.

It seems to me that if reproduction and evolution were/ could be completely independent of one another that ted definition of reproduction would be so vague such that it would have encompass systems that seen intuitively distinct from reproduction.

This is probably odd, but I am going to respond to my own question since Griesemer cleared some things up for me.

On page 82 of "Reproduction and Individuality" (from Peter Godfrey-Smith's book Darwinian Populations and Natural Selection), he writes, "And the most familiar cases of reproduction to us--human sexual reproduction--feature an obvious role for genetic novelty." However, Godfrey-Smith spends the chapter trying to account for our view of reproduction among all organisms.

It seems to me that our concept of reproduction may be tainted by our own experience. Wouldn't it be easier to start elsewhere if human reproduction is the "novelty"? The previous quote, along with the following one--"Sex tends to make reproduction clear, because the offspring cannot be a mere continuation of both parents"--made me think that perhaps we are trying too hard to base an account of reproduction that fits humanity perfectly. We should take into account that the definition of reproduction that we will end up with will be skewed from having started from the example of human sexual reproduction. Is this not important? Do we even have another option for developing this definition?


Firstly, our main scientific exploration of reproduction does not come from humans but from other animals. While we cannot quite get out of our idea of reproduction, it is a "novelty" not solely for physical reasons but mostly for social ones. This sparks another whole type of questioning about the social aspect of human reproduction.

When you make the assumption that evolution would be turned on its head I am understanding that that would only be happen because it would then suggest that there may have been a "creator" for all of life. Personally I don't think it would do anything to Evolution because there is so much more to evolution than just the ability to prove that creating life is something that was possible by someone or something else.

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Looking again at Griesemer's powerpoint, I thought that his argument goes as far as to support that selection happens at the species level or higher. I thought his examples at the end of class on Tuesday supported this argument. See power point slide examples of symbiosis and such for details and it will become apparent.

I believe that in order for a process to have material overlap, there needs to be actual physical pieces that get inherited from one point to the next. The mechanisms the virus use in order to enter its genome into that of the host's involve successive steps of replication, and the material overlap occurs when the initial virus' RNA strand leads to the final dsDNA product (the kind of A=B and B=C, so A=C relationship contains the material overlap). In the example of the photocopier, nothing is physically passed down from the original version to the copies. Explaining the sequential steps in the process that leads to a copy being made does not equate to material overlap, just some sort of temporal precedence.

I totally agree with the optimism and hope coming from synthetic biology, but perhaps with some caution when claiming that the theory of evolution is under fire. Darwin has this quote that I think is quite illuminating in regards to science as a whole, not just biology:

“As man can produce and certainly has produced a great result by his methodical and unconscious means of selection, what may nature not effect? Man can act only on external and visible characters: nature cares nothing for appearances, except in so far as they may be useful to any being. She can act on every internal organ, on every shade of constitutional difference, on the whole machinery of life.” Page 83

Specifically what I find so illuminating is that even as humans start to learn more and more of how to manipulate "nature", they can never really escape this dilemma of being part of this "nature", whether we see it or not. With the rise of medical advances some people also thought that humans were "stopping" evolution (as rudimentary definitions of selection were then being challenged), rather than just extending the form(s) it can take. Or even more frighteningly, eugenicists thought that social welfare policies were a way of preventing evolution too. I think Kropotkin's "Mutual Aid" as a dynamic of evolution seems to come to the defense of the theory of evolution whenever there is a claim to its "new" or "particular" irrelevancy.

But is synthetic biology anything more than the extension of complexity through which symbiosis can take form? Aren't there a number of species whose existence is now completely dependent on human control? This still fits a general idea of selection (who gets selected and who doesn't), why should synthetic biology be seen differently if all that is changing is HOW we control (re)production? Although the question of material overlap in this case might be under heavy stress, I don't necessarily think evolution theory is.