Concerns About the Implications of BioLogos’ Science, Pt 4

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February 12, 2011 Tags: Science & Worldviews

Today's entry was written by Ard Louis. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Concerns About the Implications of BioLogos’ Science, Pt 4

This is part four in a series taken from Louis' paper (downloadable here), which addresses common Christian misconceptions about the nature of science and its relationship to God's involvement in our world. Links to the first three parts are located on the side bar to the right.

Natural Theology and Evolutionary Metaphors

Pure chance, absolutely free but blind, is at the very root of the stupendous edifice of evolution…The ancient covenant is in pieces; man at last knows that he is alone in the unfeeling immensity of the universe, out of which he only emerged by chance.

- Jacques Monod,
"Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology", Knopf (1972)

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

- Charles Darwin, "Origin of Species" (1859)

The main message of the previous section is that Christians need to be very careful when trying to derive theological truths from the mechanisms of nature. But it is not all doom and gloom for natural theology. Alister McGrath, for example, has recently called for a renewed approach that is more sensitive to the critiques of Newman, Barth, and others:

Contrary to the Enlightenment’s aspirations for a universal natural theology, based on common human reason and experience of nature, we hold that a Christian natural theology is grounded in and informed by a characteristic Christian theological foundation. A Christian understanding of nature is the intellectual prerequisite for a natural theology which discloses the Christian God.1

There is no “view from nowhere”. So if we start from Christian presuppositions, does this make more sense of the world than other vantage points do? Does what we observe within the natural order resonate with the core themes of the Christian vision of God? This approach is potentially much more fruitful, and McGrath makes a very impressive start with his recent Gifford lectures2, which include a gentle attempt to look at biological evolution, and explore a fascinating connection to Augustinian notions of primordial actuality and emergent possibility.

Nevertheless, we probably don’t understand enough about biology to make much progress towards a detailed natural theology. That doesn’t mean that many Christians and Naturalists haven’t tried. Most popular attempts tend to flounder into some version of either God of the gaps or atheism of the gaps. One of the biggest problems is the reliance on metaphors that anthropomorphize natural processes (including evolution), and/or introduce all kinds of morally-freighted terminology.

And before we can even speak of metaphors, it is necessary to delineate what we mean by evolution. As many authors have pointed out, the word evolution has many meanings. Here is a simple taxonomy:

  1. Evolution as natural history: The earth is old and the kinds of organisms that populate our world have changed over time.
  2. Evolution as a mechanism: A combination of variation and natural selection helps explain the structure of the observed change over time in natural history.
  3. Evolution as a worldview: Evolution as a way of seeing the world and extracting meaning from it. See e.g. George Gaylord Simpson’s famous quote: Man is the result of a purposeless and materialistic process that did not have him in mind. He was not planned. He is a state of matter, a form of life, a sort of animal, and a species of the Order Primates, akin nearly or remotely to all of life and indeed to all that is material.3

Christians rightly reject definition 3. Almost all the hermeneutical tension with Scripture arises from natural history (what about Adam, the fall etc…). But as critically important as these theological issues are, I won’t treat that topic here. Nevertheless, much Christian resistance to evolution also arises from definition 2. That is the main sense in which I will be using the word when examining the following metaphors:

Random or Stochastic?

Monte Carlo algorithms that rely on random sampling are routinely used to calculate everything from the value of your stock portfolio to the airflow around a rocket returning into the atmosphere. They are part of a wider class of so-called stochastic methods. It is not hard to demonstrate that for many high-dimensional problems such stochastic methods are the most efficient solution methods available. If you view evolution as an optimization problem in a very high dimensional space, then the most efficient way to solve this problem would probably be by stochastic methods. From that perspective it is not surprising that, if God wanted a universe where biological complexity emerged through the regular ways he sustains the universe, he would employ a stochastic algorithm to achieve this goal. The problem is that the word “random variation” has all kinds of other value-laden connotations. If instead we used the technical term “stochastic variation” it could clear up a lot of confusion.

In this context it is important to emphasize that although Monte-Carlo algorithms employ stochastic methods to generate variation, they are not random in their outcomes. They converge on the desired solution only if you chose the right kinds of variation and the right kind of selection. One could, in fact, aptly employ the metaphor “survival of the fittest” to the describe the way a Monte Carlo program selects between the stochastically generated variations to solve a problem, say, in engineering, but hopefully the temptation to extract further meaning from this metaphor would be curtailed.

Self-assembly – shaking a box of Lego bricks and out comes a fully formed train?

Your body is full of intricate machinery. If you were to happen across a scaled up version of one of these machines, you’d assume that it was made by an assembly line or some other much more complex system. But in biology there are no such factories. Instead composite objects self-assemble – they make themselves. It is a little bit like having special Lego blocks. You put them in a box, shake it, and out comes a fully formed train. I’m sure most people would agree that such Lego bricks would be much more impressive than the standard ones. This self-assembly metaphor nicely captures what happens in evolution. Rather than making things fully formed, God could have used a process by which things “make themselves”.

From my lab: a picture of the self-assembly of a model T=1 icosahedral virus. Time increases from (a) –> (d). Each virus capsid is made up of 12 pentagonal bipyramids. If the interactions between the particles are designed correctly, they can be placed at random initial positions, and then move around randomly, but they nevertheless will always end up as well-formed icosahedra. The correct design depends more on the topology of the search space than it relies on the types of random (stochastic) steps available. See I. G. Johnston, A. A. Louis and J. P.K. Doye, “Modelling the Self-Assembly of Virus Capsids “, J. Phys.: Condensed Matter, 22 ,104101 (2010) for more details.

Genes as blueprints or as networks of switches?

One of the surprises that came out of the human genome project was how few genes (protein coding stretches of DNA) humans have — around 23,000, not that different compared to the fruit fly with 14,000, and quite a bit less than rice, with 51,000. Traditionally the metaphor for genes was something more akin to a blue-print, — the “standard dogma” of Francis Crick: each gene codes for one mRNA which codes for one protein — but now we realize that many are better viewed as switches or volume knobs. Moreover, one gene can have multiple effects. Complexity arises not so much from the genes themselves as from the connections between them. These network properties are currently an enormously rich topic of research. For example, the way the network is connected can dramatically affect the interplay between robustness to mutation and evolvability (the ability of a system to generate heritable phenotypic novelty). The single gene <—> single property blueprint metaphor is outdated.

Part of the transcriptional network of an E. Coli bacterium. The red dots denote proteins, and the black arrows show how the proteins are regulated by one another. Source: U. Alon.

We will look at a few more of these metaphors in the next post.

Notes

1. A.E. McGrath, The Open Secret: A New Vision for Natural Theology, Oxford: Blackwell (2008), p4

2. A.W. McGrath, A Fine-Tuned Universe: Science, Theology, and the Quest for God (2009)

3. George Gaylord Simpson, The Meaning of Evolution, Yale University Press, (1967), p. 345.


Ard Louis is a Reader in Theoretical Physics and a Royal Society University Research Fellow at the University of Oxford, where he leads a research group studying problems on the border between chemistry, physics and biology. He is also the International Secretary for Christians in Science, an associate of the Faraday Institute for Science and Religion and served on the board of advisors for the John Templeton Foundation.

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Roger A. Sawtelle - #51323

February 16th 2011

Defensedefumer,

Thank you for your remarks.

I am glad you brought up the name of Lynn Margolis.  You are right she is a wel known and excellent scientist, who has been criticized because she refuses to toe the Darwinist line.  Most scientists of her stature would be seen as leaders, but she is seen as on the fringe.  Some people just refuse to accept the evidence.

Now concerning the extinction of the dinosaurs the point is not that their extinction led directly to the modern world.  The point is that enviromental change led to significant changes in species.  Evolution is a very long process.  I appears to me that the evidence indicates that environmental changes led to the changes of species rather than the other way around. 

I agrre that it was not the dinosaurs that suppressed the mammals, but the lack of ecological niches well suited to the mammals.


Alan Fox - #51504

February 18th 2011

I appears to me that the evidence indicates that environmental changes led to the changes of species rather than the other way around.

This is exactly right. The environment (the niche) is the designer. An empty niche is a “green pasture” for an organism that happens into it. An empty niche like one of Lenski’s flasks, for example! Remember that other organisms as food, prey, predators, parasites, symbionts when present or absent form part of the niche environment. Environments are dynamic and evolutionary change can feed back into the mix.


Alan Fox - #51505

February 18th 2011

Bilbo:

Amino acids do not self-assemble into proteins.

Spider Silk

“Although different species of spider, and different types of silk, have different protein sequences, a general trend in spider silk structure is a sequence of amino acids (usually alternating glycine and alanine, or alanine alone) that self-assemble into a beta sheet conformation.”

(Follow the onward links if you don’t like Wikipedia)


John - #51586

February 18th 2011

Alan,

Bilbo is correct.

In your quote mine, the author is using a shorthand: amino acids instead of the formally correct amino-acid residues. They are no longer amino acids after incorporation into protein. The other clue that this does not contradict Bilbo’s statement is the term “sequence of” that proceeds the shorthand.

You really need to quit with the quoting. You’re coming off like an intellectually shallow creationist.


Alan Fox - #51899

February 20th 2011

Regarding self assembly of amino acids into spider silk, I was indeed wrong. The self assembly that occurs is of already assembled peptides into silk via hydrogen bonding. Apologies for my error.


Roger A. Sawtelle - #51534

February 18th 2011

Alan Fox,

Thank you for agreeing with what I call ecological or environmental natural selection, as opposed to Darwinian survival of the fittest natural selection.  I appear to have misunderstood what you were saying in the other blog because of the confusion between the two understandings of natural selection. 

Sadly Dawkins & Co hold dearly to his understanding of Darwin and this wrongheaded view has influenced science into thinking that nature is mechanistic, linear, and random, when it is actually organic, nonlinear, and nondeterminate.


John - #51585

February 18th 2011

Roger wrote:
“Darwinian survival of the ####### natural selection.”

Darwinian selection isn’t about survival, it’s about reproduction.

Really, Roger, your desperate need to make everything look like hearsay is preventing you from grasping the most fundamental concepts.


Alan Fox - #51560

February 18th 2011

Thank you for agreeing with what I call ecological or environmental natural selection, as opposed to Darwinian survival of the ####### natural selection.  I appear to have misunderstood what you were saying in the other blog because of the confusion between the two understandings of natural selection.

I think you still misunderstand my point of view. As far as I am concerned, selection by the environment involves differential ability of individuals within a breeding population to produce offspring due to variation in the phenotype which is in turn the result of genetic variation. Environmental natural selection is Darwinian. You need to explain what you see as the distinction between your “ecological selection” and “Darwinian selection”.


Jon Garvey - #51566

February 18th 2011

Is “#######” an expletive over there in the US?


Roger A. Sawtelle - #51604

February 18th 2011

Jon,

I think that maybe we just invented the pound expletive.

I am more surprised to see it than anyone.  If a word belongs there it is fittest and maybe the blog bug decided to to expunge it.


Roger A. Sawtelle - #51606

February 18th 2011

“I think you still misunderstand my point of view. As far as I am concerned, selection by the environment involves differential ability of individuals within a breeding population to produce offspring due to variation in the phenotype which is in turn the result of genetic variation.”

Alan, Alan, Alan.

Almost anyone can produce offspring.  So what?  Is the person who has 10 children 5 times fitter than one who has only 2.  Has someone who does not have any children a failure who has lived a completely purposeless life?


Alan Fox - #51643

February 19th 2011

Roger #51606

I am giving you what I hope is a mainstream summary of the mechanism of natural selection. The result is proliferation of genes within a breeding population that are more successful in a particular niche.

Almost anyone can produce offspring. So what?

The fact that organisms reproduce is important, I guess, for the resultant existence and diversity of life on Earth.

Is the person who has 10 children 5 times ###### than one who has only 2.  Has someone who does not have any children a failure who has lived a completely purposeless life?

These are philosophical questions (that, I suspect, philosophers can ask but not answer) and not at all connected with the mechanism of natural selection. They are outside the realm of science.

P S You might try a synonym for #######; I am curious what is being filtered.


Jon Garvey - #51644

February 19th 2011

Hmm - “Fitter” is filtered but “Filter” isn’t, so it must be fitter. I wonder if “Fritter” is filtered, if “Lifter” is altered or whether one could be inventive and talk of fittening, survival of the fitmost etc.

Sorry to divert the thread, but it’s difficult for you two to argue over definitions when one is defining hatch signs.


Jon Garvey - #51645

February 19th 2011

Fititude?


Roger A. Sawtelle - #51671

February 19th 2011

Jon,

It seems that every day one learns something new.  You called this # a hatch sign.  We call # the pound sign. 

Another example of England and America separated by one language?


Jon Garvey - #51675

February 19th 2011

@Roger A. Sawtelle - #51671

Over here we have survival of the £££££££. If the exchange bureau gives you #s for $s you won’t be able to buy many souvenirs!


Roger A. Sawtelle - #51676

February 19th 2011

Allan wrote:

“The result is proliferation of genes within a breeding population that are more successful in a particular niche.”

Wait a minute here.  You are back to environmental niche language which Darwinians avoid.  If the niche determines the success of the genes, as you said before and it seems here, then it is not the genes that determine the success of the life form as Lenski said.

If reproduction is the only way to advance the evolutionary process, does that mean that worker bees who cannot reproduce, but are necessary to maintain the hive and care for the queen do not play a role in the evolutionary process.  How about human beings who make discoveries that improve the lives of millions of humans, but do not reproduce.  Are they ourside the process also?


Alan Fox - #51904

February 20th 2011

Regarding Bilbo’s assertion “Amino acids do not self-assemble into proteins.” I still think this unqualified statement is incorrect.

“Amino acids can easily react with each other to form short random sequence peptides, some of which may have performed important functions in very early, primitive life forms.  Peptides can form either by drying amino acids at moderately elevated temperatures, or even by reacting with each other while dissolved in water, in the presence of certain high energy compounds such as COS, a compound found in volcanic gases.  So forming peptides is not chemically difficult.”


Alan Fox - #51911

February 20th 2011

If reproduction is the only way to advance the evolutionary process, does that mean that worker bees who cannot reproduce, but are necessary to maintain the hive and care for the queen do not play a role in the evolutionary process.

This is a fascinating subject all of its own. Google haplodiploidy and eusociality in hymenoptera for more information.


Alan Fox - #51912

February 20th 2011

How about human beings who make discoveries that improve the lives of millions of humans, but do not reproduce.  Are they ourside the process also?

Yes, obviously!


Grant Blair - #52086

February 21st 2011

Your assessment of evolutionary statistics is correct. When computing probabilities regarding Evolution, most statisticians use rectangular distributions (e.g. rolling a die). Nature (God) uses the Normal (bell curve) distribution.
Rectangular distributions have a range, but have no target value. You have an equal chance of every possible value.
Normal distributions cluster around a target value. 2/3 of the time, you will be within +/- 1 standard deviation. 95% of the time you will be within 2 standard deviations. There is only 1 chance in 20 you will will be near the extremes of your range.
In real life processes, we can move outcomes closer and closer to target by reducing the standard deviation. Small changes give you large improvements. I would argue that God does the same thing.


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