Comments on: Life with a capital L? (Like Zimmer with a capital Z?) http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/ Mon, 04 Feb 2013 17:13:44 +0000 hourly 1 http://wordpress.org/?v=3.4.2 By: The Meaning of Life « Science Picks http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17444 The Meaning of Life « Science Picks Thu, 26 Jan 2012 21:55:30 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17444 [...] Zimmer posted a response to his article from an evolutionary biologist named David Hillis that I found interesting and insightful: Like all [...] [...] Zimmer posted a response to his article from an evolutionary biologist named David Hillis that I found interesting and insightful: Like all [...]

]]> By: David Hillis http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17443 David Hillis Wed, 18 Jan 2012 04:23:08 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17443 Manda Clair Jost: Reading back through the responses, I see that I missed a question that you posed. I'd say any particular organism (like Carl Zimmer) is an individual that can only be defined ostensively. But the concept of "organism" is a class that can be defined intensionally. Like the class concept of life, different people may define this term differently, so as to arbitrarily include or exclude things like viruses as organisms. Manda Clair Jost: Reading back through the responses, I see that I missed a question that you posed. I’d say any particular organism (like Carl Zimmer) is an individual that can only be defined ostensively. But the concept of “organism” is a class that can be defined intensionally. Like the class concept of life, different people may define this term differently, so as to arbitrarily include or exclude things like viruses as organisms.

]]> By: David Hillis http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17442 David Hillis Wed, 18 Jan 2012 03:46:02 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17442 In response to C.L. Dorsch: Note that my main point was drawing the distinction between two different meanings of the word "life" that are often confused. One is the biological taxon we call Life with a capital "L", which, like other such entities, can only be "defined" ostensively. I think this is the meaning that most people (or at least most biologists) have in mind when they use the word "life". Like other biological taxa, Life can be diagnosed or characterized, but that is not the same as a definition, and those attributes are not necessarily requirements of its recognition. [Consider another example of a "characteristic" that is not a requirement: we say that limbs are "characteristic" of the taxon Tetrapoda, but many tetrapods (like snakes) have lost their limbs. I'd say that the same thing applies the "characteristic" of Life as cellular; viruses are parts of Life that have lost cellularity.] Hence, there is an ostensive "definition" of Life in the Tree of Life Appendix I referenced (pointing to the largest monophyletic group on the Tree of Life), followed by a list of the characteristics (a diagnosis) we commonly use to recognize Life. I also noted that it is certainly possible to define an unbounded (in space and time) class concept of life (with a small "l"), which may apply to other entities that are similar to Life on Earth. But, I'd argue, any such concept is bound to be an arbitrary class, rather than a natural class, so I doubt that any definition will satisfy everyone. In the end, different people will recognize things that are more or less similar to Life, and call them living, or not. My point was that there is not a right or wrong answer...there are just entities (known or imagined) that are similar to Life in varying degrees. The sooner we recognize the subjective nature of this problem, the sooner we can put this "problem" behind us. Then, we can realize the potential for a whole range of possible entities that are similar to Life in varying degrees. If we discover a part of Life (big L) on another planet (which I'd say is unlikely, but possible), then that will be relatively easy to determine, and certainly surprising (unless we've put it there). Much more likely is that we'll discover something SIMILAR to Life...and the fun part will be learning HOW similar it is, not arguing about whether it should be called alive or not. The first is discovery and science, whereas the second is quibbling over semantics. Personally, I think finding anything even remotely similar to Life on another planet would be exciting. If and when we do make that discovery, I suspect that this entire discussion will become a lot clearer to many people. In response to C.L. Dorsch: Note that my main point was drawing the distinction between two different meanings of the word “life” that are often confused. One is the biological taxon we call Life with a capital “L”, which, like other such entities, can only be “defined” ostensively. I think this is the meaning that most people (or at least most biologists) have in mind when they use the word “life”. Like other biological taxa, Life can be diagnosed or characterized, but that is not the same as a definition, and those attributes are not necessarily requirements of its recognition. [Consider another example of a "characteristic" that is not a requirement: we say that limbs are "characteristic" of the taxon Tetrapoda, but many tetrapods (like snakes) have lost their limbs. I'd say that the same thing applies the "characteristic" of Life as cellular; viruses are parts of Life that have lost cellularity.] Hence, there is an ostensive “definition” of Life in the Tree of Life Appendix I referenced (pointing to the largest monophyletic group on the Tree of Life), followed by a list of the characteristics (a diagnosis) we commonly use to recognize Life.

I also noted that it is certainly possible to define an unbounded (in space and time) class concept of life (with a small “l”), which may apply to other entities that are similar to Life on Earth. But, I’d argue, any such concept is bound to be an arbitrary class, rather than a natural class, so I doubt that any definition will satisfy everyone. In the end, different people will recognize things that are more or less similar to Life, and call them living, or not. My point was that there is not a right or wrong answer…there are just entities (known or imagined) that are similar to Life in varying degrees. The sooner we recognize the subjective nature of this problem, the sooner we can put this “problem” behind us. Then, we can realize the potential for a whole range of possible entities that are similar to Life in varying degrees. If we discover a part of Life (big L) on another planet (which I’d say is unlikely, but possible), then that will be relatively easy to determine, and certainly surprising (unless we’ve put it there). Much more likely is that we’ll discover something SIMILAR to Life…and the fun part will be learning HOW similar it is, not arguing about whether it should be called alive or not. The first is discovery and science, whereas the second is quibbling over semantics. Personally, I think finding anything even remotely similar to Life on another planet would be exciting. If and when we do make that discovery, I suspect that this entire discussion will become a lot clearer to many people.

]]> By: Jess Tauber http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17441 Jess Tauber Tue, 17 Jan 2012 01:23:48 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17441 Should nanobes ever become established as a real form of life we would have to add a fifth group, after viruses (unless you are willing to say that the viruses that infect eukaryotes, eubacteria and archaea are themselves different lineages that just share trimmed down parasitism (and what about giant viruses, or viruses that infect other viruses, and viroids???). Should nanobes ever become established as a real form of life we would have to add a fifth group, after viruses (unless you are willing to say that the viruses that infect eukaryotes, eubacteria and archaea are themselves different lineages that just share trimmed down parasitism (and what about giant viruses, or viruses that infect other viruses, and viroids???).

]]> By: C.L. Dorsch http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17440 C.L. Dorsch Mon, 16 Jan 2012 12:11:14 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17440 Professor Hillis (in Carl Zimmer’s formulation) writes: “Like all historical entities (including other biological taxa), it is only sensible to “define” Life ostensively (by pointing to it, noting when and where it began, and following its lineages from there) rather than intensionally (using a list of characteristics). This applies to the taxon we call Life (hence capitalized, as a formal name).” In the comments Professor Hillis recommends we view the companion website to ‘The Principles of Life’ at http://bcs.whfreeman.com/hillis1e/#667501__674516__ where we can see brief descriptions of taxa. Doing so one discovers, by clicking on “the taxon we call Life,” this text: “Characterized by a nucleic-acid based genetic system (DNA or RNA), metabolism, and cellular structure.” (The taxon of Life “characterized by,” and not “life” “defined by,” I am quick to point out.) I am innocent in these things, but I wonder how much of Professor Hillis’s preferred reticence about speaking of “life” (as opposed to “Life”) flows from an implicit presumption that the extended creature we know on this planet as Life is most likely, not only in the peculiarities of its ramifications, but in its basic mechanisms, Earth specific. The implication seems to be that any other “similar” creature we come across in another setting will be a creature of a different sort. (We leave aside the possibility of still undiscovered taxa distinct from “Life” inhabiting this planet.) It seems to me that it is this sense of the uniqueness of terran Life that leads Professor Hillis to otherwise disdain speaking of life generally. And in this sense, as a particular creature with a distinct history and character, Life is indeed a singular thing – like Carl Zimmer. But so, of course, by definition, is every other of the myriad creatures, entities, or configuration or constellation of entities in existence. All actual “things” are in this sense “bounded” or “historical.” The dust mote floating past me as well as the Milky Way bending across the night sky are bounded historical entities not amenable to “definition.” “Things” are not amenable to definition, and Life (as taxon) being an evident thing, cannot be so treated. This, of course, was no one’s intention, as I far as I can tell. But “life”? This is “unbounded” – it is a notion, a class, a set, an abstraction. It, in the terms here, is certainly formally amenable to definition, but, alas, we seem to have only one instance of it, that being Life, the terran creature. How does one define the set rules for a set which has only one member? Is that a pointless exercise? Can we only point at this unique creature, reduced to watching and describing it being born, feed, metabolize, reproduce and die? Two thoughts: One regards what seems to be Dr. Hillis’s operant assumption that “similar life” if found will be significantly distinct from terran Life. This does indeed seem to be an outcome more imagined now than it was only a few generations ago, but that is, it seems, speculative. Given the knowledge at hand I am not aware how this likelihood could be demonstrated to be any more probable than the likelihood that there are presently millions (or billions) of planets currently occupied by creatures “characterized by a nucleic-acid based genetic system (DNA or RNA), metabolism, and cellular structure.” Not that I am necessarily inclined to the latter likelihood, but only noting that there is no presently known evidentiary indication contradicting the equivalence of earth Life with any supposed universal life. Second is simply that an obvious approach to defining the set rules for a set which has only one member is merely to query the uniqueness which has led, even tentatively, to the construction of that set. As the wise man said “One of these things is not like the others, one of these things just doesn't belong.” What are the attributes that led to the contradistinction of “life” in the first place, the setting aside of the notion of “the living”? This is what defines the class as we know it. It may not be a useful definition for either discovering the “life-like” in other contexts, or otherwise have great value outside the vernacular, but it certainly isn’t some sort of categorical impossibility. And in those terms the results of Trifonov’s sieve – self-reproduction with variation – doesn’t seem so far off the mark to me. In the end, while knowledge of the relevant possibilities or probabilities may still be well beyond us, we are nonetheless not constrained, by either biological fact or semantic procedure, from tentative definition. We are likely to be mistaken, as we usually are, and there’s a good chance that our thinking may serve as much as a stumbling block as an opening, but we need not remain mute, merely pointing to what, in any event, we still do not yet understand. Professor Hillis (in Carl Zimmer’s formulation) writes:

“Like all historical entities (including other biological taxa), it is only sensible to “define” Life ostensively (by pointing to it, noting when and where it began, and following its lineages from there) rather than intensionally (using a list of characteristics). This applies to the taxon we call Life (hence capitalized, as a formal name).”

In the comments Professor Hillis recommends we view the companion website to ‘The Principles of Life’ at http://bcs.whfreeman.com/hillis1e/#667501__674516__ where we can see brief descriptions of taxa. Doing so one discovers, by clicking on “the taxon we call Life,” this text: “Characterized by a nucleic-acid based genetic system (DNA or RNA), metabolism, and cellular structure.” (The taxon of Life “characterized by,” and not “life” “defined by,” I am quick to point out.)

I am innocent in these things, but I wonder how much of Professor Hillis’s preferred reticence about speaking of “life” (as opposed to “Life”) flows from an implicit presumption that the extended creature we know on this planet as Life is most likely, not only in the peculiarities of its ramifications, but in its basic mechanisms, Earth specific. The implication seems to be that any other “similar” creature we come across in another setting will be a creature of a different sort. (We leave aside the possibility of still undiscovered taxa distinct from “Life” inhabiting this planet.)

It seems to me that it is this sense of the uniqueness of terran Life that leads Professor Hillis to otherwise disdain speaking of life generally. And in this sense, as a particular creature with a distinct history and character, Life is indeed a singular thing – like Carl Zimmer. But so, of course, by definition, is every other of the myriad creatures, entities, or configuration or constellation of entities in existence. All actual “things” are in this sense “bounded” or “historical.” The dust mote floating past me as well as the Milky Way bending across the night sky are bounded historical entities not amenable to “definition.” “Things” are not amenable to definition, and Life (as taxon) being an evident thing, cannot be so treated.

This, of course, was no one’s intention, as I far as I can tell.

But “life”? This is “unbounded” – it is a notion, a class, a set, an abstraction. It, in the terms here, is certainly formally amenable to definition, but, alas, we seem to have only one instance of it, that being Life, the terran creature. How does one define the set rules for a set which has only one member? Is that a pointless exercise? Can we only point at this unique creature, reduced to watching and describing it being born, feed, metabolize, reproduce and die?

Two thoughts:

One regards what seems to be Dr. Hillis’s operant assumption that “similar life” if found will be significantly distinct from terran Life. This does indeed seem to be an outcome more imagined now than it was only a few generations ago, but that is, it seems, speculative. Given the knowledge at hand I am not aware how this likelihood could be demonstrated to be any more probable than the likelihood that there are presently millions (or billions) of planets currently occupied by creatures “characterized by a nucleic-acid based genetic system (DNA or RNA), metabolism, and cellular structure.” Not that I am necessarily inclined to the latter likelihood, but only noting that there is no presently known evidentiary indication contradicting the equivalence of earth Life with any supposed universal life.

Second is simply that an obvious approach to defining the set rules for a set which has only one member is merely to query the uniqueness which has led, even tentatively, to the construction of that set. As the wise man said “One of these things is not like the others, one of these things just doesn’t belong.” What are the attributes that led to the contradistinction of “life” in the first place, the setting aside of the notion of “the living”?

This is what defines the class as we know it. It may not be a useful definition for either discovering the “life-like” in other contexts, or otherwise have great value outside the vernacular, but it certainly isn’t some sort of categorical impossibility. And in those terms the results of Trifonov’s sieve – self-reproduction with variation – doesn’t seem so far off the mark to me.

In the end, while knowledge of the relevant possibilities or probabilities may still be well beyond us, we are nonetheless not constrained, by either biological fact or semantic procedure, from tentative definition. We are likely to be mistaken, as we usually are, and there’s a good chance that our thinking may serve as much as a stumbling block as an opening, but we need not remain mute, merely pointing to what, in any event, we still do not yet understand.

]]> By: David B. Benson http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17439 David B. Benson Sun, 15 Jan 2012 06:18:22 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17439 No definition is as yet entirely satisfactory. Ian Stewart tries his hand in "The Mathematics of Life" and then considers some of the difficulties. By the way, Koonin in his "The Logic of Chance" also considers viruses as life forms; doesn't mentions prions one way or the other. No definition is as yet entirely satisfactory. Ian Stewart tries his hand in “The Mathematics of Life” and then considers some of the difficulties.

By the way, Koonin in his “The Logic of Chance” also considers viruses as life forms; doesn’t mentions prions one way or the other.

]]> By: Steve Flinn http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17438 Steve Flinn Sat, 14 Jan 2012 15:24:39 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17438 Generalizing Shannon, biological life as a process (vs. the state of being alive) can be defined as a communications coding process that maximizes the probability of continuity of information propagation through the time-based, unbounded channel over time. See: http://www.steveflinn.com/Evolution_as%20Communication_MW-AS103%2003-29-06.pdf Generalizing Shannon, biological life as a process (vs. the state of being alive) can be defined as a communications coding process that maximizes the probability of continuity of information propagation through the time-based, unbounded channel over time.

See:
http://www.steveflinn.com/Evolution_as%20Communication_MW-AS103%2003-29-06.pdf

]]> By: David Hillis http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17437 David Hillis Sat, 14 Jan 2012 01:36:23 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17437 OK, but the example still seems to hold...I wasn't discussing identifying the consciousness of either Carl Zimmer or of Life, but rather their physical existence as real things. As such, Carl Zimmer still serves as a useful example of an individual. OK, but the example still seems to hold…I wasn’t discussing identifying the consciousness of either Carl Zimmer or of Life, but rather their physical existence as real things. As such, Carl Zimmer still serves as a useful example of an individual.

]]> By: Manda Clair Jost http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17436 Manda Clair Jost Fri, 13 Jan 2012 17:03:26 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17436 Hi David! I like your inclusion of viruses in Life, due to their probable descent from the LUCA. But under your arguments for both Life and Zimmer, I wonder if you think the general term "organism" (not a taxon) should also be understood by ostensively referring to individual examples, rather than defining the term "organism" as a particular type of entity with certain attributes. Each organism, of course, is also a historical phenomenon (like Carl Zimmer). But how can we refer to examples of historical entities like organisms unless we have defining criteria allowing us to recognize them as such? Does this ostensive world view have a place or a use for the term "organism"? My guess, David, is that you might view an Organism as something like an irreducible branch or tip of Life – but that is about as satisfying to me as a concept of a "star" with no defining characteristics other than the fact that it is a component of the historical entity known as the "universe". Thoughts? Hi David! I like your inclusion of viruses in Life, due to their probable descent from the LUCA. But under your arguments for both Life and Zimmer, I wonder if you think the general term “organism” (not a taxon) should also be understood by ostensively referring to individual examples, rather than defining the term “organism” as a particular type of entity with certain attributes. Each organism, of course, is also a historical phenomenon (like Carl Zimmer). But how can we refer to examples of historical entities like organisms unless we have defining criteria allowing us to recognize them as such? Does this ostensive world view have a place or a use for the term “organism”?
My guess, David, is that you might view an Organism as something like an irreducible branch or tip of Life – but that is about as satisfying to me as a concept of a “star” with no defining characteristics other than the fact that it is a component of the historical entity known as the “universe”. Thoughts?

]]> By: Wzrd1 http://blogs.discovermagazine.com/loom/2012/01/11/life-with-a-capital-l-like-zimmer-with-a-capital-z/#comment-17435 Wzrd1 Fri, 13 Jan 2012 16:49:40 +0000 http://blogs.discovermagazine.com/loom/?p=5420#comment-17435 Honestly, I doubt that I'll live to hear a final definition of life. I remember when bacteria was accepted as life, but the humble virus was a heated debate. A cancerous cell is considered life. One definition was, consuming, excreting and reproduction. But, if that is true, one could call a prion alive, as it consumes compounds and excretes itself (as well as apparent toxic effects) and most certainly reproduces. It's widely accepted that prions are not life, but merely a malfunctioning protein that causes disease. If we have difficulty with ascertaining what life is and defining it, how CAN we define a complex organism like a Carl Zimmer? Indeed, one goes into some of the heavier philosophical questions that are thousands of years old. And when we go there, we always end up with, I think I think, therefore, I think I am. I think. Honestly, I doubt that I’ll live to hear a final definition of life. I remember when bacteria was accepted as life, but the humble virus was a heated debate. A cancerous cell is considered life.
One definition was, consuming, excreting and reproduction. But, if that is true, one could call a prion alive, as it consumes compounds and excretes itself (as well as apparent toxic effects) and most certainly reproduces.
It’s widely accepted that prions are not life, but merely a malfunctioning protein that causes disease.
If we have difficulty with ascertaining what life is and defining it, how CAN we define a complex organism like a Carl Zimmer? Indeed, one goes into some of the heavier philosophical questions that are thousands of years old.
And when we go there, we always end up with, I think I think, therefore, I think I am.
I think.

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