Defining life in a world without Darwin

_{Denyse O'Leary

July 12, 2011

Origin Of Life}

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At one time, life was simple, and defining it was easy. NASA defined life as: “a self-sustained chemical system capable of undergoing Darwinian evolution.” [1] In that case, what are they to make of recent findings that life’s simplest cells evolve mainly by swapping genes, and not through Darwinian competition? [2] Can they forbid teaching that in publicly funded schools – Texas Darwin lobby-style? But then …

Don Johnson, author of Probability’s Nature and the Nature of Probability offers, on the definition of life:

Although there is no universally accepted definition of life [3], it often includes characteristics like metabolism, growth, adaptation, and reproduction. The existence of a genome and the genetic code divides living organisms from nonliving matter is perhaps the most concise definition of life. [4]

Concise yes, and it offers no theory of origin. Thoughts?

[1]The wording is attributed to OOL researcher Gerald Joyce, in Foreword, Origins of Life: The Central Concepts, D.W. Deamer and G R Fleischaker, editors (Boston: Jones & Bartlett; 1994). pp. xi–xii. This article from the NASA Astrobiology Institute: Leslie Mullen, “Unfamiliar Life: Why should the particular polymer combinations of Earth reign supreme?” (April 17, 2002) The definition seems to have been accepted.

[2] “Microbes evolve predominantly by acquiring genes from other microbes, new research suggests, challenging previous theories that gene duplication is the primary driver of protein evolution in prokaryotes”, from Megan Scudellari Gene swap key to evolution: Horizontal gene transfer accounts for the majority of prokaryotic protein evolution, The Scientist ( 27th January 2011)

[3] Claus Emmeche, “DefiningLife, Explaining Emergence,” 1997.

[4] Hubert Yockey, Information Theory, Evolution, and the Origin of Life, 2005. This definition includes as living (or at least as once living) organisms those that are sterile (e.g. mules and worker ants) and those not having cells (e.g. viruses). While life uses the laws of chemistry and physics, those laws cannot define or explain life any more than the rule of grammar that were used during the preparation of this book define its content. (P. 18)

Comments

Doveton, do you know what the phrase patently false means?Mung_{July 13, 2011
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1) Science isn’t about belief and requires no belief Patently false.
I have no doubt that you believe such, Mung, but declarations without substantiation don't carry much weight or credibility. You are, of course, welcome to your opinion however.Doveton_{July 13, 2011
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1) Science isn’t about belief and requires no belief Patently false.Mung_{July 13, 2011
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Elizabeth Liddle:
Mung:
Why should we believe your unfalsifiable theory?
First, you shouldn’t believe any theory, you should simply evaluate whether it is a good fit to the data. (snip} Third, as I’ve said before, science does not, in fact, proceed by falsification (except of the null, which doesn’t count) – it proceeds by fitting models to data, then using the fitted model to predict new data. Also by comparing fits of alternative models.
Nicely put, Dr. Liddle! These two are, imho, the foundations of really understanding science. 1) Science isn't about belief and requires no belief; it is about utility - what explanations are useful for predicting further aspects of our world's phenomena. 2) Scientific utility comes from the models describing how a given phenomenon works. Models are refined as more evidence becomes available. Models that do a better job of describing how a given phenomenon or set of phenomena operate are used more often (and sometimes replace*) older models. * I particularly enjoy Isaac Asimov's The Relatively of Wrong for its clarity on this subject. A worthwhile read for those who have not done so: http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htmDoveton_{July 13, 2011
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... you know, the metaphysical equivalent to empty calories.Ilion_{July 12, 2011
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"What’s up with that?" Just her way of letting me know to generally skip over any post of hers.Ilion_{July 12, 2011
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junk, the stuff about the flagellum was in the comments, not a post.WilliamRoache_{July 12, 2011
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Junkdnaforlife,
The amount of effort that people spend trying to stop the idea of ID speaks volumes.
Yes indeed! 538 separate blog posts regarding ID available to anybody with an internet connection speaks volumes of the lengths those pesky darwinists will go to to suppress dissenting thought!WilliamRoache_{July 12, 2011
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I also found it interesting that (at telic thoughts) the category with the most entries is Intelligent design coming in with a whopping 538. Coming in second was a category named "The debate", with 325 entries. And coming in third, strangely, was "evolution," with 308. The amount of effort that people spend trying to stop the idea of ID speaks volumes.junkdnaforlife_{July 12, 2011
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WilliamRoache, I just checked the blog and could not find the flagellum evolution post. Drop a link and I will check it out. I found this I thought was funny. A commenter posted this:
The ideas of directed evolution, sequence mutation, and tailoring presented above lend naturally to more global concepts of design involving the notion of energy landscapes. For proteins, statistical-mechanic frameworks based on density of states, pioneered by Frauenfelder, Wolynes, Dill, Onuchic, Thirumalai and others (e.g.,[70–72]), have been invaluable in interpreting various protein kinetics and thermodynamic observations such as conformational sub-states, folding mechanisms, and function. Recently, Pitt and Ferre-D’Amare[73 ] introduced the notion of empirical RNA fitness landscapes by a combination of experiment and computation to analyze the optimization of typical SELEX products in terms of sequence/function relationships for small RNAs (up to 13 nt). Such genotype/phenotype mapping is of general interest and practical importance.
http://monod.biomath.nyu.edu/index/papdir/fulllengths/2011Curr.pdf Commenter then wrote this:
I think it is rather obvious the authors of the paper were thinking along the lines of human "directed evolution" and human "design", but I'm in a bit of a trouble-making mood, so I thought I would stir things up a bit. I am also posting this on Panda's Thumb. link I'm not an expert here and am willing to have it explained to me how I got this wrong.
-- It's funny, the ID debate, the virus that it, is everywhere lol.junkdnaforlife_{July 12, 2011
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Mung:
Why should we believe your unfalsifiable theory?
First, you shouldn't believe any theory, you should simply evaluate whether it is a good fit to the data. Second, not all predictions arising from theory are unique. So just because your theory predicts something that another theory predicts as well doesn't mean that your theory has no predictive power - it just means that the prediction in question doesn't distinguish the two theories. I've noticed this come up before - someone (me, for example) points out that an observation claimed to be a problem for Darwinism actually isn't, and the comeback is: well, that means Darwinism explains nothing. No, it doesn't. It means that the observation in question is compatible with Darwinism Not the same thing. Third, as I've said before, science does not, in fact, proceed by falsification (except of the null, which doesn't count) - it proceeds by fitting models to data, then using the fitted model to predict new data. Also by comparing fits of alternative models. The reason the falsification criteria (in its probabilistic sense) is still a bit relevant as a criterion for whether a theory is scientific is that a theory should both explain existing data and make predictions regarding new data that differ from rival theories. Darwin's theory does this. However, in science, as soon as you get confirmatory data the first thing you ask is: is there yet another alternative theory that might account for these new data? And so on. It's an iterative process. And often how it works is that the original theory becomes progressively refined, giving rise to nested sub-theories, as well as super-theories that extend beyond it, and account for data that the original theory doesn't explain. You might even say that it's the signature of a good theory. Darwin's was, and is, a good theory.Elizabeth Liddle_{July 12, 2011
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Mung:
Elizabeth, an an earlier thread you argued that evolution does not take place at the level of the cell.
I argued that natural selection takes place at the level of the organism - the phenotype.
And yet here you are arguing that it does. What’s up with that?
Because for microbes, the cell is the level of the phenotype.Elizabeth Liddle_{July 12, 2011
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Mung, Our understanding of evolution is also evolving. It would be odd if it were not. So the roots of the tree become bushes, some things are reclassified etc etc. Boring housekeeping work really for a living theory still in it's infancy (given that we'll probably be studying our biological inheritance on this planet for our entire history). So, no, Mung, the theory does not fit "any data". If we were to sequence a polar bear and find Pi encoded to a million bits in it's DNA evolution would not "fit" around that. If Irreducible Complexity really was a problem for evolution (it was predicted many years ago btw by a "darwinist") then it would have been a problem for evolution. But it was not. As Nick is showing on Telic Thoughts at the moment the evolution of the flagellum is now well supporter in the literature and no ID in sight. That the denizens of TT object furiously does not matter a whit. Their objections can be sent to the publisher of the paper in question. So go on then. What's the number one data point that you say should have broken evolution wide open rather then being noted and adjustments made (kinda like the borg!)?WilliamRoache_{July 12, 2011
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Elizabeth, an an earlier thread you argued that evolution does not take place at the level of the cell. And yet here you are arguing that it does. What's up with that?Mung_{July 12, 2011
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Why don't I believe in a theory that can fit any data?Mung_{July 12, 2011
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Mung, Why don't you simply "believe" in the theory that fits the data best? PS You don't believe in theorems the same way that people believe in religion. It's to do with supporting evidence and all that sort of thing. It's not really a question of "belief" if something is supported by verifiable facts.WilliamRoache_{July 12, 2011
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Why should we believe your unfalsifiable theory?Mung_{July 12, 2011
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You write:
In that case, what are they to make of recent findings that life’s simplest cells evolve mainly by swapping genes, and not through Darwinian competition?
These are not mutually exclusive! What evidence do you have that the results of gene-swapping never result in differential reproduction?Elizabeth Liddle_{July 12, 2011
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