Why Up When Down is Just As Good And A Lot Easier?

_{Barry Arrington

March 25, 2013

Intelligent Design}

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Phinehas asks Neil Rickert a fascinating question about the supposed direction of evolution. Neil says he will address it in a separate thread, and I started this one for that purpose. The rest of the post is Phenehas’ question to Neil:

@Neil I also appreciate the professional tone. I am a skeptic regarding what evolution can actually accomplish. In keeping with your demonstrated patience, I’d be grateful if you would give serious consideration to something that keeps tripping me up. I’ve often thought of natural selection as the heuristic to random mutations’ exhaustive search.

A path-finding algorithm can be aided in finding a path from point A to point B by using distance to B as a heuristic to narrow the search space. Without a heuristic, you are left to blind chance. It is said that evolution has no purpose or goal, so there is no point B. It is also claimed that evolution isn’t simply the result of blind chance, so a heuristic would seem to be required. Somehow, natural selection is supposed to address both of these concerns. Nature selects for fitness, we are told, so somehow we have a heuristic even without a point B.

But what is fitness? How does it work as a heuristic? How is it defined? Evidently, it is all about reproductive success. But how does one measure reproductive success? This is where things get fuzzy for me. Surely evolution is a story about the rise of more and more complex organisms. Isn’t this how the tree of life is laid out? Surely it is the complexity of highly developed organisms that evolution seeks to explain. Surely Mt. Improbable has man near its peak and bacteria near its base. But by what metric is man more successful at reproducing than bacteria? If I am a sponge somewhere between the two extremes, how is a step toward bacteria any less of a point B for me than a step toward man? Why should the fitness heuristic prefer a step upward in complexity toward man in any way whatsoever over a step downward in complexity toward bacteria?

It seems that, under the more obvious metrics for calculating reproductive success, bacteria are hard to beat. Even more, a rise in complexity, if anything, would appear to lead to less reproductive success and not more. So how can natural selection be any sort of heuristic for helping us climb Mt Improbable’s complexity when every simpler organism at the base of the mountain is at least as fit in passing on its genes as the more complex organisms near it’s peak? And without this heuristic, how are we not back to a blind, exhaustive search?

Comments

@Neil
My own way of looking at evolution, is in terms of a population. I see the population as exploring the environment (or the fitness landscape, as it is sometimes called). I see the production of mutations as part of this exploration.
For me, the problem of the cookie cutter analogy isn't that the dough has to be forced through the cookie cutter, but that the cookie cutter is designed to pretty much the same degree (and maybe more so?) that you would need to design the cookie itself in order to get the same shape. My apologies if the following is a weak analogy, but it is what springs to mind. (BTW, I thought your travel analogy was perfectly fine in explaining what you wanted to explain, I just didn't think it helped me understand what I wanted to understand.) As I've said, it is the elegance and accuracy of macroevolution that I find difficult to understand from a purely chance-based or naturalistic perspective. While the appeal to natural selection seems a plausible heuristic at first blush, a closer examination reveals it to be lacking in explanatory power. So maybe it is the fitness landscape that provides accuracy where natural selection cannot? I find the game of golf and getting a ball from the tee to the hole a decent analogy for understanding the elegance and accuracy that I'm talking about. (As an aside, I still think I would describe the duffer's game as less elegant than the pro's, and might point to the hours spent on the practice tees as an indication to the behind-the-scenes complexity of the pro's game.) From a microevolutionary perspective, I can imagine the Darwinist setting a golf ball on the side of a hill, carefully propped up by a single blade of grass. After a while, a gust of wind starts the ball rolling down hill, naturally. "See," says the Darwinist, "Now imagine more of that!" OK. I can imagine more wind, earthquakes, hills, etc. But it is the accuracy of the overall tale of the ball getting from the tee to the hole that still nags at me. "No problem," says the Darwinist, "its not so much about random forces like the wind as it is about the landscape." So he sets about constructing a mini-golf-course hole with windmills and water hazards and carefully calculated angles. He sets the ball on the tee, and after another gust of wind, sure enough, the ball rolls down a hill, around the water hazard, through the windmill, bounces off the angled brace, and drops into the hole. You see, whenever I start thinking about fitness landscapes and environmental niches and the like, the only way I can get any sort of accuracy out of it (like the accuracy of a big, fat arrow pointing unerringly toward greater complexity) is if the fitness landscape itself is designed for that accuracy. In other words, the "mutations" in the external environment would appear, under purely natural circumstances, to be just as random as those in the cell. So appealing to the environment looks like it just moves the problem back a step. And in the end, I end up right back at pure, blind chance performing an exhaustive search. Where am I going wrong?Phinehas_{March 26, 2013
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Michael Beha on Dollo's Law and why evolution shouldn't be expected to be time-asymmetric. http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim026721.htmltragic mishap_{March 26, 2013
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@John W Kelly
Because the life giving Light comes down to Earth from the heavens and generates a Common Ascent of increasingly complex creations.
(Some posts are difficult to interpret on the internet, where there is often little context from which to view a snippet like this, so please forgive me if I've got this all wrong.) It appears that you are trying to support Darwinian evolution by appealing to a negative argument of a religious nature. Is that right? This seems a strange choice if there are plenty of positive scientific arguments for Darwinism at hand.Phinehas_{March 26, 2013
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@Nick
Imagine a planet covered with only bacteria-like cells. If one cell were bigger, and thus more slowly reproducing, but was able to eat the other bacteria, would it persist in the ecosystem? Your argument says no. Which is why your argument is ridiculous.
First of all, I'm not presenting an argument so much as asking questions. I honestly don't understand, but would like to. Second, it appears once again that what I'm getting at is a bit too subtle, since it has obviously been misunderstood. I'll try to clarify. I'm imagining your planet covered in bacteria-like cells. I'm also imagining a larger, predatory cell introduced into the environment. I have no problem imagining that predator persisting in the environment. I can also imagine it eating all of the other prey cells and then starving into extinction. Or eating only the local prey cells and then going extinct because it didn't have the mobility to reach additional food sources. Or mutating to have the mobility and surviving. Or the prey cells also gaining mobility and the predator going extinct. I can even imagine predator an prey having a race to the top of the food chain. Or not. (As a video game designer, I have an active imagination. Seriously, I can do this all day.) In fact, I bet I could imagine an evolutionary story to fit just about any data. None of this really addresses my question, though it may suggest new ones. The main thing I still don't get it how natural selection can save evolution from a blind/exhaustive search of the problem space. When all is said and done and all the stories have been told, lowly bacteria still exist, and by most if not all of the metrics for actually calculating reproductive fitness, they are more fit than the increasingly complex organisms that came after them. So how can selection via reproductive success save the evolution of complexity from a blind search at the macro level when more complex organisms appear to be, if anything, less successful? Why shouldn't man be at the bottom of the tree of life and bacteria at the top, if the story of evolution is all about reproductive success? Even if we drop back to the micro level and consider that first predatory cell that we imagined, how did its ability to eat other cells arise, other than by blind chance? And if macroevolution is simply more microevolution, then how is it not blind chance all the way down?Phinehas_{March 26, 2013
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footnotes to post 39 as to the exponentially worse problem that 'context dependency' presents to the evolvability of novel functional protein sequences:
Coherent Intrachain energy migration at room temperature - Elisabetta Collini and Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/
Here are two other ways to deduce 'context dependent' quantum information along the entire protein structure:
Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/ Proteins with cruise control provide new perspective: Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” http://www.princeton.edu/main/news/archive/S22/60/95O56/
The preceding experiment is solid confirmation that far more complex functional information resides along the entire protein structure than meets the eye.,, For a sample of the calculus equations that must be dealt with to calculate ‘cruise control’ please see this following site:
PID controller Excerpt: A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. http://en.wikipedia.org/wiki/PID_controller
It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure 'quantum form' is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale within proteins, for how can the quantum entanglement 'effect' in proteins possibly be explained by a material (matter/energy) 'cause' when the quantum entanglement 'effect' falsified material particles as its own 'causation' in the first place?
Quantum Entanglement – The Failure Of Local Realism - Materialism - Alain Aspect - video http://www.metacafe.com/w/4744145 Qubits that never interact could exhibit past-future entanglement - July 30, 2012 Excerpt: Typically, for two particles to become entangled, they must first physically interact. Then when the particles are physically separated and still share the same quantum state, they are considered to be entangled. But in a new study, physicists have investigated a new twist on entanglement in which two qubits become entangled with each other even though they never physically interact.,, http://phys.org/news/2012-07-qubits-interact-past-future-entanglement.html Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012) Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed. Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,, The remaining option is to accept that (quantum) influences must be infinitely fast,,, “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,, http://www.sciencedaily.com/releases/2012/10/121028142217.htm
Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has already been falsified by the very same effect you are seeking to explain! Improbability arguments of various 'special' configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!bornagain77_{March 26, 2013
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Wow, an evo from another forum chimed in and sed:
And here I thought it was the explanation for the prevalence of nested hierarchies
Just about anything can be put into a nested hierarchy Henry J. For example an Army can be placed into a nested hierarchy. And an Army doesn't have anything to do with common descent nor evolution.Joe_{March 26, 2013
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NR:
As I see it, a scientific theory serves two roles. One of those is as a guide to research. I’m not a biologist, however neo-Darwinism seems to be doing pretty well as a guide to research. It establishes technical terminology and gives direction to the research.
Except neo-darwinism isn't even a theory. It can't even muster a testable hypothesis. NR:
Natural selection is often presented as a kind of filter that shapes the direction of evolution.
If whatever survives to reproduce is a direction.Joe_{March 26, 2013
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Mr. Fox as to:
,,“Climbing Mount Improbable”. As it happens, I was re-reading it a fe days ago,,
Here is a excellent video excerpt from 'Darwin's Dilemma' (also listed) which clearly gets to the thrust, and crushing critique, of Dawkins' argument:
"Climbing Mount Improbable" - Evolution Vs. Functional Proteins - Where Did The Information Come From? - Doug Axe - Stephen Meyer - video http://www.metacafe.com/watch/4018222/ Darwin's Dilemma - Excellent Cambrian Explosion Movie http://www.youtube.com/watch?v=KWEsW7bO8P4
Just how 'small' are these steps up the 'backside of 'Mount Improbable' that Dawkins envisions?
Doug Axe PhD. on the Rarity and 'non-Evolvability' of Functional Proteins - video (notes in video description) http://www.metacafe.com/watch/9243592/ When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide "Biologist Douglas Axe on Evolution's (non) Ability to Produce New (Protein) Functions " - video Quote: It turns out once you get above the number six [changes in amino acids] -- and even at lower numbers actually -- but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth. http://intelligentdesign.podomatic.com/entry/2012-10-15T16_05_14-07_00 "a very rough but conservative result is that if all the sequences that define a particular (protein) structure or fold-set where gathered into an area 1 square meter in area, the next island would be tens of millions of light years away." Kirk Durston
Moreover, The "context dependency" of any particular sequence of amino acids is found to exponentially exasperate the incremental evolution of protein sequences for Darwinists:
(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics - 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions.pdf "Why Proteins Aren't Easily Recombined, Part 2" - Ann Gauger - May 2012 Excerpt: "So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required." http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2
Moreover, many proteins are multifunctional and, serendipitously, perform several different 'context dependent' tasks within the cell, thus further exasperating the problem for Darwinists:
Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought: Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. http://www.sciencedaily.com/releases/2008/11/081102134623.htm Genes Code For Many Layers of Information - They May Have Just Discovered Another - Cornelius Hunter - January 21, 2013 Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms."
Throw in Dr. Behe's work on HIV and Malaria, etc.., and the 'context dependency' problem becomes even worse for Darwinists. But Mr. Fox, what is all this 'context dependency' found for proteins really telling us about the inadequacy of the molecular reductionism of Darwinism? The following article gives us a strong clue as to how we should be actually be viewing the proteins within cells in the 'context of life':
Epigenetics and the "Piano" Metaphor - January 2012 Excerpt: And this is only the construction of proteins we're talking about. It leaves out of the picture entirely the higher-level components -- tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players. http://www.evolutionnews.org/2012/01/epigenetics_and054731.html
bornagain77_{March 26, 2013
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I really like Tim's story about the 'beer-swilling amoeba'. You can easily see the advantage in reproduction that a beer swilling amoeba would have over a sober one. As the saying goes 'I never went to bed with an ugly ameoba but have woken up with plenty' ;)PeterJ_{March 26, 2013
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Surely Mt. Improbable has man near its peak and bacteria near its base. But by what metric is man more successful at reproducing than bacteria?
Just wondering if you'd read "Climbing Mount Improbable". As it happens, I was re-reading it a fe days ago and I didn't notice Dawkins make any such point.Alan Fox_{March 26, 2013
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Phinehas - Coming from the field of physics I have always thought about this lack of direction in evolution in terms of the problem of the perpetual motion machine. A naive person can think. Oh let's build a perpetual motion machine this way. 1. We line up bowls of water on a set of steps. 2. We wait for the natural process of evaporation and condensation to move the water up the steps. 3. We let the water flow back down to the bottom bowl through a turbine to create energy. 4. We use this as an infinite source of energy. What the naive person fails to realize is the "natural process of evaporation and condensation" would be just as good at moving water from an upper bowl to a lower bowl as lower bowl to upper bowl. You get a random walk, not a directional flow. So if evolution is fine with a random walk, what they need is a series of fits and starts. First evolution builds up quite a bit of life, then the whole thing collapses. Then it builds up a little more, then it all collapses. The idea of a random walk having any direction to it is an inherent contradiction. This is why the "bowls of water on steps" fails as a perpetual energy source. And it is why evolution fails. An evolutionist who believes in a random walk of life must believe in a series of directionless steps ( some towards more complex life, some towards simpler life). The current situation of the biosphere is just a great big step in the "more complex" direction. The problem is that no evolutionist can actually believe this. There is little confidence that neo-Darwinist techniques can build up the current biosphere along a directed route in the short time allotted by the universe. How much less credible is the idea that the entire biosphere has been built up to the current level of complexity by some random oscillations about some equilibrium state. Evolution is nonsense and most people realize it. It takes obfuscation, special pleading, belief in directionless direction, and ignoring of large inherit self inconsistencies to accept it. No wonder the Psalmist wrote, "The fool has said in his heart, there is no God."JDH_{March 25, 2013
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Why Up When Down is Just As Good And A Lot Easier? Because the life giving Light comes down to Earth from the heavens and generates a Common Ascent of increasingly complex creations. #TMOGJohn W Kelly_{March 25, 2013
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Neil, you may be happy to learn that I am not going to pile on about how lame your analogy is. I'll with-hold my opinion of your analogy for now, in fact, for the sake of argument, I'll try to track with it. In your analogy, the best you seem to be saying is that fitness is somehow analogous to your travelogue being shared. In other words, a longer pleasant trip is more likely to be recorded and shared than an unpleasant trip. We all get how there is no travel agent in your story, but what you haven't explained is why there is travel in your story. Traveling is dangerous(!) even in your own analogy (cf. "unpleasant trips"). So, suppose you are an beer-swilling amoeba. An amoeba because it was mentioned earlier, and beer-swilling because it implies that you are fat, happy, and just ready to reproduce. I'd ask why in the world would you expend unimaginable resources to go climb Mount Improbable or any of the other Rocky Mountains. Your analogy suggests that you just got a wild hair and did it. This can only be analogous to a random mutation of some sort. But at 21, WJM writes, "If fitness means anything along the lines of hardiness that increases ongoing reproductive success, then evolution apparently started out with pretty much the most fit organism possible and everything went downhill from there. Human beings, then, don’t exist because of Darwinistic evolution; they exist in spite of it" I'd say he has hit the nail right on the head. Amoebas like to drink beer. It makes them better amoebas. Even it they "wanted" (mutated) to travel, they are better at beer. WJM used hardiness; I'll use robustness. Fitness, whatever fitness is, requires them for enough time for organisms to reproduce. (I learned that in a BIOLOGY BOOK.) Robust amoebas are robust because they apply the resources they have appropriately; taking trips would not seem to fit. This is what people want you to address. Why would an amoeba sitting in a recliner with a beer on his belly, travel at all, risking death, spending resources that would otherwise be used on, well, beer, instead of just getting better at simply drinking beer? It isn't enough to say that the rest of the world was getting more complex. First of all, that assumes facts not in evidence, and second of all, many species when faced with an increasingly complex environment merely drink more beer. It is what they know . . .Tim_{March 25, 2013
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well lifepsy, darwinists never had any evidence that genes and/or proteins could arise incrementally anyway! i.e. if substantiating evidence doesn't really matter to your 'scientific' theory in the first place,, what difference is it if you just 'randomly' allow stuff to poof into existence?,, I mean as long as it is not Intelligence ever doing the 'poofing' it is still science is it not?? :)
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen. Richard Lewontin's January 9, 1997 article, Billions and Billions of Demons
bornagain77_{March 25, 2013
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bw(10) http://www.biomedcentral.com/1471-2164/14/117/abstract
CONCLUSIONS: We suggest that the overall trends of gene emergence are more compatible with a de novo evolution model for orphan genes than a general duplication-divergence model. Hence de novo evolution of genes appears to have occurred continuously throughout evolutionary time and should therefore be considered as a general mechanism for the emergence of new gene functions.
Yup, Orphans. That whole evolutionary model of functional sequences being selected for in small increments is no good anymore. Evolution works by poofing new genes into existence, now. Blind natural forces are great at that sort of thing. This is the mother of all ad-hoc explanations. Anyone want to place bets on when we might be lucky enough to observe any new orphan genes popping into existence?lifepsy_{March 25, 2013
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My final comment for today (Mar 25, Chicago time). I'll be back tomorrow. There have been questions about Darwinism. Since I am not a Darwinist, I'm the wrong person to ask. But I'll at least say a little. As I see it, a scientific theory serves two roles. One of those is as a guide to research. I'm not a biologist, however neo-Darwinism seems to be doing pretty well as a guide to research. It establishes technical terminology and gives direction to the research. A second role for a theory, is as a marketing instrument to sell the science to those outside the field. And, as I see it, Darwinism does that rather poorly. There's a tendency to dismiss that problem, by blaming it on creationists. However, some non-religious folk have similar objections and similar misunderstandings of evolution, so I think it fair to say that Darwinism is not very effective at selling the theory to people outside of biology. Natural selection is often presented as a kind of filter that shapes the direction of evolution. As an analogy, imagine a cookie cutter that shapes the cookie dough. The trouble with a cookie cutter, is that it is passive. The cook has to force the dough through the cookie cutter before there is any shaping. Natural selection has a similar problem. And what forces biological populations through the shaping of natural selection, is the biological reproduction. I see too much emphasis on selection (sometimes criticized as pan-selectionism or pan adaptionism), and not enough emphasis on the importance of pressures caused by reproduction. Biologists know all about reproduction, but they make the mistake of not saying enough about its role when talking to the lay public. My own way of looking at evolution, is in terms of a population. I see the population as exploring the environment (or the fitness landscape, as it is sometimes called). I see the production of mutations as part of this exploration. I'm not sure why, but many scientists don't want to look at it that way, because they think it looks too much like purposeful activity, and they want to avoid "purpose" and other terms in the intentional vocabulary. However, you cannot avoid the intentional vocabulary. Biology is loaded with apparently purposeful behavior. On the question of complexity vs. simplicity, I'm surprised at the disagreement. Yes, the space station is complex, because the problem is complex. But, given the complexity of the problem, the solution is relatively simple. Phinehas mentions a golf game, so I'll suggest that the path that the ball takes from the tee-off to the hole will usually be more complex when a duffer is playing, than when a pro is playing. Since the topic of fitness has come up, I'll comment on that tomorrow (again, as a non-biologist).Neil Rickert_{March 25, 2013
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Nick Matzke:
Imagine a planet covered with only bacteria-like cells.
Who are you, Rod Serling?
If one cell were bigger, and thus more slowly reproducing, but was able to eat the other bacteria, would it persist in the ecosystem?
No, because I can imagine the other bacteria ganging up on that one and eating it.Joe_{March 25, 2013
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"Fitness" = "Whatever quality makes a Darwinian just so story sound the most plausible."William J Murray_{March 25, 2013
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'evolution is really a superstitious, dirt-worshiping religion, i.e., a religion of cretins, created by cretins for cretins.' Don't put yourself down, Mapou. That must be the gold standard of epigrammatically dimissive eloquence. Brutally blunt though it be, within the context it has its own beauty. 'a religion of cretins, created by cretins for cretins.' I believe the Greeks considered a circle, the perfect, shape, and there is a wonderful, circularity, parsimony and balance about that last phrase of yours. And 'a dirt-worshipping religion' is simply overkill, an embarrassment of riches. All worthy of the Encyclopaedia Britannica, although I am not absolutely certain the editors would concur. It meets Einstein's aesthetic criterion for selecting hypotheses. Though it may be that I'm just dazzled by the euphony. But I don't think so.Axel_{March 25, 2013
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Nick, If one prebiotic organization of some unknown sort didn't benefit from a mechanism to establish the semiotic relationships required to record information into a medium (and then translate effects from it), and another did...which one would be able to evolve via changes to that information?Upright BiPed_{March 25, 2013
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Mr. Matzke you claim that a bigger and slower reproducing organism can be considered 'more fit' if the bigger organism eats the smaller but faster reproducing organism, but what prevents these faster, smaller, reproducing organisms from eating the larger, slower, reproducing ones?
Richard Dawkins interview with a 'Darwinian' physician goes off track - video Excerpt: "I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly -- a few hours sometimes, they can reproduce themselves -- that they can evolve very, very quickly. And we're stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?" http://www.evolutionnews.org/2012/07/video_to_dawkin062031.html
A stunning example of that paradoxical scenario was played in HIV Mr. Matzke: Michael Behe defends the one 'overlooked' protein/protein binding site generated by the HIV virus, that Abbie Smith and Ian Musgrave had found, by pointing out it is well within the 2 binding site limit he set in "The Edge Of Evolution" on this following site:
Response to Ian Musgrave's "Open Letter to Dr. Michael Behe," Part 4 "Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane --- not something to crow about after 10^20 replications and a greatly enhanced mutation rate." http://behe.uncommondescent.com/2007/11/response-to-ian-musgraves-open-letter-to-dr-michael-behe-part-5/
In fact, I followed this debate very closely and it turns out the trivial gain of just one protein-protein binding site being generated for the non-living HIV virus, that the evolutionists were 'crowing' about, came at a staggering loss of complexity for the living host it invaded (People) with just that one trivial gain of a 'leaky cell membrane' in binding site complexity.
"the AIDS virus originated relatively recently, as a mutation from SIV, the simian immuno-deficiency virus. According to Wikipedia, this virus was also benign in its original form:.. Unlike HIV-1 and HIV-2 infections in humans, SIV infections in their natural hosts appear in many cases to be non-pathogenic. Extensive studies in sooty mangabeys have established that SIVsmm infection does not cause any disease in these animals, despite high levels of circulating virus." https://uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/#comment-448372
Thus the 'evolution' of the virus clearly stayed within the principle of Genetic Entropy since far more functional complexity was lost by the living human cells it invaded than was ever gained by the non-living HIV virus. A non-living virus which depends on those human cells to replicate in the first place. Moreover, while learning HIV is a 'mutational powerhouse' which greatly outclasses the 'mutational firepower' of the entire spectrum of higher life-forms combined, for millions of years no less, and about the devastating effect HIV has on humans with just that one trivial binding site being generated, I realized if evolution were actually the truth about how life came to be on Earth then the only 'life' that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the 'fittest' are allowed to survive. Yet instead of eating us, or just killing us outright, which is what one would rightfully expect in a Darwinian view of things, time after time these different types of microbial life are found to be helping us in essential ways that have nothing to do with their ability to successfully reproduce,,,
NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012 Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival. http://www.nih.gov/news/health/jun2012/nhgri-13.htm We are living in a bacterial world, and it's impacting us more than previously thought - February 15, 2013 Excerpt: We often associate bacteria with disease-causing "germs" or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.,,, I am,, convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens." http://phys.org/news/2013-02-bacterial-world-impacting-previously-thought.html#ajTabs The Microbial Engines That Drive Earth’s Biogeochemical Cycles - Falkowski 2008 Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. - Paul G. Falkowski - Professor Geological Sciences - Rutgers http://www.genetics.iastate.edu/delong1.pdf
Though most people think of viruses as being very harmful to humans, the fact is that the Bacteriophage (Bacteria Eater) virus, in the preceding video, is actually a very beneficial virus to man to keep certain populations of bacteria in check.
Bacteriophage Excerpt: Bacteriophages are among the most common biological entities on Earth,,,They have been used for over 60 years as an alternative to antibiotics in the former Soviet Union and Eastern Europe.[5] They are seen as a possible therapy against multi drug resistant strains of many bacteria.,,,development of phage therapy was largely abandoned in the West, but continued throughout 1940s in the former Soviet Union for treating bacterial infections, with widespread use including the soldiers in the Red Army—much of the literature was published in Russian or Georgian, and unavailable for many years in the West. Their use has continued since the end of the Cold War in Georgia and elsewhere in Eastern Europe.,,,In August, 2006 the United States Food and Drug Administration (FDA) approved using bacteriophages on cheese to kill the Listeria monocytogenes bacteria, giving them GRAS status (Generally Recognized As Safe).[10] In July 2007, the same bacteriophages were approved for use on all food products.[11] Government agencies in the West have for several years been looking to Georgia and the Former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, e.g., Anthrax, Botulism. http://en.wikipedia.org/wiki/Bacteriophage Viruses: A Pirate Phage Commandeers the Immune System of Bacteria - Feb. 27, 2013 Excerpt: The study provides the first evidence that this type of virus, the bacteriophage ("phage" for short), can acquire a wholly functional and adaptive immune system. The phage used the stolen immune system to disable -- and thus overcome -- the cholera bacteria's defense system against phages. Therefore, the phage can kill the cholera bacteria and multiply to produce more phage offspring, which can then kill more cholera bacteria. The study has dramatic implications for phage therapy,,, http://www.sciencedaily.com/releases/2013/02/130227134334.htm
supplemental note:
Doug Axe: Lignin & the Coherent Design of the Ecosystem - podcast Excerpt: Lignin provides a paradoxical case for the Darwinian method of evolution, but fits perfectly into a design oriented scientific paradigm. Thirty percent of non-fossil organic carbon on the planet is lignin, so in a Darwinian world, something should have developed the ability to consume lignin--but it hasn't. Lignin binds together and protects plant cellulose, which is vital to all types of large plant life; "The peculiar properties of lignin therefore make perfect sense when seen as part of a coherent design for the entire ecosystem of our planet." http://www.idthefuture.com/2012/08/doug_axe_lignin_the_coherent_d.html
bornagain77_{March 25, 2013
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Nick Matzke, would you care to give us your definition of 'fitness'?Box_{March 25, 2013
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Nick @22: Way to go. You've misrepresented his argument. Of course your comment is evolutionist bluff #1. There are niches. They must get filled. Except when they don't get filled. Reproduction might drive change. Except when it doesn't. And so it goes . . . And you still haven't provided the slightest reason for why anyone should believe that such a process would drive evolution toward greater complexity of structure, less reproduction, expenditure of resources on activities unrelated to reproduction, and so on. All decent questions related to Phineas' larger inquiry. Because at the end of the day all you've got is that Great Evolutionary Explanation: Stuff Happens.Eric Anderson_{March 25, 2013
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WJM @21, I also made the point at least once before, but never as a standalone challenge. From my perspective, if one begins with a stable self-replicator, then such an entity exists in a stable state, where perturbations to its configuration, namely mutations, are much more likely to damage its ability to reproduce than to enhance it. In this stable state, natural selection can be readily observed, imo, because offspring with mutations that cause deleterious effects are unlikely to reproduce effectively, and therefore will not usually pass along their genes. Now, assuming that our first self-replicator is not optimal, we can presume that some chance mutations might occur which help optimize it, allowing for increased reproductive success to gain a foothold in the overall population. But it seems to me that such optimizations only serve to push our putative protocell upwards on a local maximum, stranding it upon a peak of the functional landscape. One consequence of this view is that for unguided evolution to have occurred gradually, multiple disparate starting points are required for early organisms, so that they can all make their way to their respective peaks on the fitness landscape. It doesn't appear that evolution by natural selection, acting necessarily upon slight changes, can jump between peaks. So either is required multiple starting points, which is reminiscent of special creation, or the ability to span great gaps of form and function, which is reminiscent of discrete miracles. The other option asks for us to imagine that increased complexity is collinear with increased fitness, at least in some environmental niche or another; and that increases in complexity can happen gradually enough for random variations to account for them, but not so gradually as to be invisible to natural selection.Chance Ratcliff_{March 25, 2013
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But what is fitness? How does it work as a heuristic? How is it defined? Evidently, it is all about reproductive success. But how does one measure reproductive success? This is where things get fuzzy for me. Surely evolution is a story about the rise of more and more complex organisms. Isn’t this how the tree of life is laid out? Surely it is the complexity of highly developed organisms that evolution seeks to explain. Surely Mt. Improbable has man near its peak and bacteria near its base. But by what metric is man more successful at reproducing than bacteria? If I am a sponge somewhere between the two extremes, how is a step toward bacteria any less of a point B for me than a step toward man? Why should the fitness heuristic prefer a step upward in complexity toward man in any way whatsoever over a step downward in complexity toward bacteria? It seems that, under the more obvious metrics for calculating reproductive success, bacteria are hard to beat. Even more, a rise in complexity, if anything, would appear to lead to less reproductive success and not more. So how can natural selection be any sort of heuristic for helping us climb Mt Improbable’s complexity when every simpler organism at the base of the mountain is at least as fit in passing on its genes as the more complex organisms near it’s peak? And without this heuristic, how are we not back to a blind, exhaustive search?
Imagine a planet covered with only bacteria-like cells. If one cell were bigger, and thus more slowly reproducing, but was able to eat the other bacteria, would it persist in the ecosystem? Your argument says no. Which is why your argument is ridiculous. Reason for creationist silliness #2847285 -- total failure to think about ecological niches. At least it's a refreshing departure from reason for creationist silliness #1 -- total failure to think statistically. Or #2: total failure to think over many orders of magnitude of timescale, geographic scale, organism size scales, etc.NickMatzke_UD_{March 25, 2013
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I've made this same argument many times. If fitness means anything along the lines of "hardiness that increases ongoing reproductive success", then evolution apparently started out with pretty much the most fit organism possible and everything went downhill from there. Human beings, then, don't exist because of Darwinistic evolution; they exist in spite of it.William J Murray_{March 25, 2013
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"Yet if natural selection has any heuristic or any big, fat arrow of its own (labelled “Increasing Fitness,” natch) at best you could say that this arrow was orthogonal to an increase in complexity, and it certainly appears that it could actually be pointing in the exact opposite direction. So how can the second be any sort of an aid or explanation for the first? Is there some way to define increasing fitness such that increasing complexity would be a natural result?"
This is an excellent question. Why should an increase in complexity correspond to an increase in fitness, viewing fitness as a measure of reproductive success? The question suggests that increased complexity, as observed, slows reproduction and makes survival more tentative. I suppose a putative answer would need to have something to do with environmental pressures, niches, fitness landscapes, etc., i.e., the usual suspects. However it should be addressed, that if fitness is measured by differential reproductive success, why should the complexity observed in multicellular, sexually reproducing organisms logically come about, when such organisms might be deemed less fit by the most useful definition of fitness. As corollaries, what slight successive changes can theoretically be introduced into bacterial organisms that would tend toward increased complexity while providing increased fitness along the way? What environmental pressures and factors may be introduced to bacterial colonies which would equate increasing complexity with reproductive success? Box @14, good quote! :)Chance Ratcliff_{March 25, 2013
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semi related: Coming in June, a Game-Changing New Book: Darwin's Doubt, by Stephen Meyer Excerpt: For now but not for long, exclusively at DarwinsDoubt.com, you can preorder your copy, receiving a steep discount, free shipping and four free digital books! http://www.evolutionnews.org/2013/03/coming_in_june070501.htmlbornagain77_{March 25, 2013
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Here are a few questions that have been on mind for quite a while. I had hoped to get satisfactory answers but to no avail. 1. How did "primitive" organisms evolve the complex ability to reproduce if this very ability is an essential prerequisite of the evolution process? 2. Given that the number of deleterious random mutations is greater than the number of beneficial random mutations by orders of magnitude (ask any programmer), how did "primitive" organisms survive the onslaught of deleterious mutations without first evolving a gene repair mechanism? 3. How does an evolved gene repair mechanism distinguish between a good and a bad mutation? These unanswered questions are why I maintain that evolution is really a superstitious, dirt-worshiping religion, i.e., a religion of cretins, created by cretins for cretins. Sorry to be so brunt. Just my opinion.Mapou_{March 25, 2013
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@bw I'm a video game designer with just enough programming knowledge to make the thought of giving me code access terrify the engineers. Still, I wrote code for Djikstra, A* and various other methods for solving well defined problems while in school. I realize that these are probably poor analogies for natural selection, but for the life of me, I just can't figure out how to view natural selection from any perspective that would save evolution from an exhaustive search of the problem space. I'm hoping someone can help me out with that.Phinehas_{March 25, 2013
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