Jul 27 2009
Evolving Useful Bacteria
Genetically modified bacteria are already a common and useful component of chemical production. Many drugs, food additives, and industrial chemicals are churned out by engineered bacteria in large vats. Bacteria are little protein and chemical factories and we put them to good use.
But engineering a strain of bacteria to do exactly what we want is laborious and expensive. Traditionally engineers have tweaked one or two genes at a time and then looked for the results. But the production of many substances by bacteria may be controlled by 20 or more genes, and so the permutations of various mutations are enormous – too many to test individually.
But now genetic engineers have developed a new technique known as MAGE – multiplex automated genome engineering. What they do is to essentially evolve bacteria with optimized or at least greatly improved production of the substance of interest. The technique causes bacteria to rapidly mutate – causing thousands of mutations and billions of different strains.
This technique allows us to do some amount of rapid evolution,” says Harris Wang, a researcher at Harvard Medical School, who led the project along with colleagues Farren Isaacs and George Church.
They then select for the strains that produce the most of whatever they are looking for. Wang and Isaacs use lycopene as an example. Conveniently, lycopene stains bacteria red, so they can just select the reddest strains. For other end products other markers will have to be used. For example, for some protein products genetic engineers have incorporated bits of DNA into the target gene that produce fluorescence, so that the cells that glow the most have the highest concentration of the target protein.
This technology has a great deal of promise, as does anything that makes it cheaper and faster for industrial development of new products and methods. In addition to speeding up the production of new drugs, it may help our quest for biofuels. Some scientists think that biofuels may be a solution to our dependence on fossil fuels. Biofuel crops can be homegrown and they are a renewable resource. However, if we use existing farmland and farm crops this will raise the price of food, and corn and other such crops are not efficient sources of biofuel – it is still debatable if they even produce as much energy as they consume.
Attention is therefore shifting to biomass that has a higher energy density, a higher crop density (more biomass per acre), is currently a crop waste product (like stalks) or grows wild (like switchgrass). The problem with these sources of biofuel is that we need to develop an industrial process that can convert the tough fibers into ethanol – in a massive and cost effective way. Economics and scale are the keys – if it costs too much to make the biofuel, it won’t happen on a large scale while gasoline is relatively cheap.
While there are many research programs going on right now, no one has developed a complete and cost effective industrial scale process for extracting biofuel from switchgrass or a similar source. One of the best hopes, however, is bacteria. If we can engineer a bacteria to eat the grass and produce some substance, like ethanol or something close to ethanol, that can then be easily refined into biofuel, we are off to the races.
Since optimization of yield and efficiency is key to the success of any such process, the MAGE technique may prove essential to the success of biofuels.
The MAGE technique is also interesting because it is a direct application of evolutionary principles. The process works by increasing diversity randomly through mutations and then selecting those bacteria that by chance have the desirable trait. This clearly demonstrates that the two step process of evolution – random diversity and selection – works.
Creationists have argued that evolution cannot work because random mutation cannot provide specificity and direction, and that selection cannot increase information because it is a negative process – it only removes information. This argument is nothing but a diversion from logic and reality, however. It should be obvious that mutations increase information and selection provides non-random specificity and direction.
In response to MAGE as an example of evolutionary principles, creationists are likely to argue that the MAGE technique allows for the inclusion of genetic mutations already known to be desirable into the mix – including introducing genes from other species. So the diversity does not have to be entirely random. But even when it is, the process still works. Also, the selection is artifical, not natural. This is an old objection by creationists to artificial selection as an analogy of evolution. This is a non sequitur, however – the analogy is that selection can drive non-random change in a randomly varying system. It doesn’t matter if the selection is artificial or natural, all that matters is differential survival.
By itself, of course, MAGE does not prove that evolution is true. No single line of evidence can do this. But is does support basic evolutionary principles with a practical application. Creationists often charge that evolution has no practical application, as if utility is a marker of scientific truth. Not only is this argument fallacious, it is factually incorrect.Creationists excel at being wrong in two or more ways simultaneously. At least they are good at something.
89 Responses to “Evolving Useful Bacteria”
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The MAGE technique is clearly a substantial step forward in evolving microorganisms to have a particular trait. I’m totally jealous of the ingenuity of this project. A few technical challanges remain that has plague strain evolution programs from the beginning, no matter the technique.
1. A robust screening method is required. Lycopene is convenient since it is a vibrant red color. Biofuel production may be limited to screening for advantageous mutations that enhance metabolism of a particular carbon source (i.e. growth improvement). Selecting for an end product like butanol will probably have to be coupled with a selection criteria like enhanced growth, somehow. Specialty chemicals that have no inherent unique chemical property to aid screening will be very challenging to evolve.
2. Not all microorganisms are as easily genetically manipulated as E. coli and S. cerevisiae (the logical next organism to test with this technique). Future adaptations will require likely require the use of viruses to deliver the ssDNA fragments.
All in all, this likely to be huge.
Sorry, but in the changing view of more and more biologists, this doesn’t work “by increasing diversity randomly through mutations and then selecting those bacteria that by chance have the desirable trait.” And this does NOT “clearly demonstrate that the two step process of evolution – random diversity and selection – works.”
This more likely is an example of directed mutation, such as referenced here:
http://www.science-frontiers.com/sf064/sf064b07.htm
The creationist are full of crap, but not because they are wrong about directed mutation. What they are wrong about is that it’s not directed by the supernatural, but that it’s becoming more and more evident that life can and often does direct, in one form or another, its own mutations.
A more up to date paper on the subject is here: http://www.jstor.org/pss/2097219
There are numerous other links I could give, but anyone really interested can find the relevant material.
Here’s one I especially liked:
http://www.pnas.org/content/99/4/2164.full.pdf+html
artfulD – the references you cite do not support your apparent position. At best adaptive mutation is a minority hypothesis that has not taken root, and there are non-adaptive explanations for putative cases. You are citing a controversial notion as if it is already generally accepted.
Also – even if it were true that in some cases mutations are triggered by environmental stress, that still would not make it the dominant mode in evolutionary change, nor would it mean that random mutations followed by selection would not work, as you seem to indicate above.
To quote your reference: “The directed mutation hypothesis has not fared well; many examples of apparently directed mutation have been rejected in favor of more conventional explanations, and several reviews questioning the validity of directed mutation have appeared.”
Yes, I tried not to be one-side in my references, because the point was not that directed mutation is as yet fully accepted – it was that your argument that this experiment clearly demonstrates that random diversity and selection works is not supported by this example. If anything, it demonstrates one way that life itself can direct mutation, leaving open the question of how pervasive the process may be.
Also I have never indicated that random mutations and selection would not work. My position has always been that this is not the only way that selection works. Randomness really explains nothing – it simply posits that at bottom everything has happened by accident. It doesn’t explain at all how life has taken advantage of those accidents.
How does this example show that life can direct mutations? The process involved generating billions of strains and then selecting the few that happen to have the desirable trait. There is nothing to indicate that the mutations are anything but random. This does not include, as I said, when they use the technique to incorporate specific genetic sequences – but that is no directed mutation either, it’s genetic engineering.
Well first of all the generation of those strains was deliberately caused by a life form we designate as human.
And I’d argue that genetic engineering is also a form of mutation in that it’s the changing of the structure of a gene.
Of course if you define mutation as the process of random change, then you will seem to have eliminated direction from the definition. But you won’t have eliminated it from consideration as part of the evolutionary process.
A couple things I think should be clarified pertaining to MAGE before this example is used too broadly as support for whatever idea.
For lycopene production:
i) 20 genes were selected for up regulation i.e. increased metabolic activity, and 4 genes were targeted for deletion. They did this by designing each ssDNA to bind SPECIFICALLY to a region in the genome. Therefore, they knew exactly which genes would change and how they would change. What is random is they pooled the 24 ssDNA fragments and the combination of the changes to those 24 genes is random, i.e. 0, 1, 2, 3, ect genes can be affected and in different combination. Therefore, the potential total number of combinations is 24^24.
ii) the lycopene selection criteria was not a selective pressure, i.e. changes made did not necessarily give the E. coli growth advantages. Therefore, if total pool of E. coli mutants were allowed to continuously grow and not subjected continuously forced to mutate, the original wildtype E. coli strain has a better chance of becoming the dominant strain. Basically, if lycopene was not red in color, they would have had to test THOUSANDS of mutants individually to find the strains with the desired phenotype.
iii) If absolutely no information was known about lycopene biosynthetic pathway, this procedure would not be applicable. And there is no way for the researchers to know if any other genes are involved in improving lycopene production through this method. Using a chemical mutagen or UV radiation are traditionally used methods to randomly affect the ENTIRE genome. MAGE is like using one or more guided missile to random hit a number of specified targets while a mutagen is like dropping a few unguided bombs and praying they hit the right building(s) within a huge city.
The example of the 30 year experiment to evolve an E. coli strain capable of growing on citric acid is more suited to argue against Creationists. I know this is a favorite example of Dr. N.
Draal – you are correct, and I was thinking of the citrine example.
But let’s be clear on what I was saying – I acknowledge this is artificial selection. And also this is not cumulative selection as would be seen in natural evolution and as was seen in the citrine example.
This technique targets genes, and can even introduce new genetic material. But what it does show is that mutations – even artificially created one – can be used to effectively increase information by generating new strains, and then selection can be used to target the ones that happen to have the specific desirable trait(s). This counters the information arguments of the ID crowd. It does not prove evolution as there are many other aspects of organic evolution not relevant to these experiments.
So while your points are valid, they were not points I was making in the first place.
Regarding the definition of “mutation” – it is only a change in the genetic code. Mutations can be spontaneous or induced, they can be random or non-random.
In nature we know that random spontaneous mutations occur, and there is no reason why such mutations would not add to genetic information and provide raw material for selection.
How much of evolution is due to that vs epigenetic factors or mutations that occur in response to general or specific environmental stress and also to cross-species genetic mobility (like viral inclusions) remains to be seen. My perception is that the consensus is still that random mutations combined with natural selection is the dominant mode of evolution, even though these other processes are also taking place. If this is no longer the consensus I would happily change my opinion to match the new consensus of scientific opinion – but I would need to see some references, and the ones shown so far don’t cut it.
*cough* citrate *cough* not citrine *cough cough*
Citrine is a form of quartz.
Yes, but it doesn’t demonstrate that it’s only a two step process, because as you are now acknowledging, the consensus is that this particular theory of the process is dominant but not exclusive of other theoretical processes. And some of these other processes – and you have pointed to several – are already seen as more than hypothetical.
I actually have a large file of references that, while they act to support my biases, probably won’t do much to change yours.
But here’s something along these lines that I found marvelously persuasive:
http://www.kcl.ac.uk/ip/davidpapineau/Staff/Papineau/OnlinePapers/SocLearnBald.htm
That link should be:
http://www.kcl.ac.uk/ip/davidpapineau/Staff/Papineau/OnlinePapers/SocLearnBald.htm
Here’s something on the above writer’s credentials:
http://www.kcl.ac.uk/schools/humanities/depts/philosophy/people/academic/papineaud/
When did I say “only”, or “exclusive” and why would assume I have any bias in this question? I seek only to understand the consensus of scientific opinion.
And yes, I meant citrate, thanks.
You say a lot by inference, and here’s an example: “So the diversity does not have to be entirely random. But even when it is, the process still works.”
Well maybe it does and maybe if it has always been a directed process, then it doesn’t.
And everyone who says they are inclined to agree with a consensus has a bias toward consensus being persuasive. Granted yours is toward scientific consensus and is a quite reasonable position, but a bias nevertheless. Where might you, or I for that matter, have stood prior to the advent of Darwinism, for example.
:S
Let me see if I understand this: The Baldwin effect was an attempt to explain situations like Darwin’s Galapagos finches. It’s a way of reconciling how multiple traits can emerge in one subspecies.
When isolated and over time, a particular subspecies can emerge and be dominant (selective pressure). Subspecies can also emerge in the same locale as they fill in niches (also selective pressure).
I like Belyaev’s experiment with silver foxes to explain how dogs evolved from wolves.
By selecting just for one trait, multiple traits emerged at once. In the case of the silver foxes, smaller adrenaline glands made the foxes more tame. At the same time, the coats of the foxes began to change color. This was because adrenaline shares the biological pathway for making the melanin responsible for different colors of fur. So, not only did they select for a docile fox, they also accidentally created foxes with different coat colors. Changes in hormone levels can have cascading effects that show up as multiple changes in phenotype.
http://www.gmilburn.ca/2009/03/20/clever-as-a-fox/
He also experimented on rats, otters, and minks.
http://www.nytimes.com/2006/07/25/health/25rats.html?ex=1311480000&en=ee8f5fbaf0576814&ei=5090&partner=rssuserland&emc=rss
Well, as the cited article stated, “The Baldwin effect occurs, if it ever does, when a biological trait becomes innate as a result of first being learned.” So if that’s the nexus of the process, then of course it would explain how subspecies will almost have to emerge when the differing environments are causative in the learning of new strategies – and those strategies (if you accept that life forms are basically strategic entities) would necessarily require changes in the entity’s physiological structure.
And to posit that learning results in heritable strategic differences doesn’t mean that the entity had any idea of the specificity of the changes that would result. Directed consequences have a persistent way of being unintended.
And in the case of dogs, they were clearly bred with strategic purposes in mind, with no initial forewarning that a change in strategy would necessitate unpredictable changes in the the dog’s physiology. Although a consequence may then have been the breeding of dogs to maintain that seemingly beneficial physiology which at the same time often screwed up the dog’s ability to perform in accordance with its strategic purposes.
Cascading effects indeed.
ArtfulD, I don’t know if we are on the same page. You’re saying a learned behavior can cause a permanent change in a population?
The strategy purpose of all organisms is to survive and reproduce. Changes to DNA that result in changes in the phenotype are selected for by pressures. Not all genotype changes are manifest in changes of the phenotype; as exemplified by dominant and recessive genes. Multiple phenotypes can arise from a single change in genotype.
In the case of the silver foxes and dogs, changes that affected their ability to produce adrenaline affected their behavior. It wasn’t their behavior that changed their genes.
Draal, that’s too simple. The common purpose may be to survive and reproduce, but the strategy of each organism to deal with the problems along the way will differ according to its niche, its competition, predation, available energy supply, type of supply, anticipated seasonal changes, ad infinitum. Even if one doesn’t accept the premise of the Baldwin effect, this has to be the case.
More on this later as I’ve just been called on to do a chore elsewhere.
All those are directly related to survival.
Niche: (ecology) the status of an organism within its environment and community (affecting its survival as a species)
Competition: (Ecology) The simultaneous demand by two or more organisms for limited environmental resources, such as nutrients, living space, or light.
Predation: The capturing of prey as a means of maintaining life.
Survival is also dependent on food availability and climate.
Survival is the common thread with all of them mentioned. How they go about doing it is the beauty of genetic diversity. More than one tool can serve to perform the same task.
OK, back again. When you speak of pressure, part of that pressure involves the need to change what has become a relatively unworkable strategy. But these changes are very slow in organisms with longer generational spans compared to those with almost no generations in their existence at all – no learning curves, no herd, swarm or shoaling cultures, no nurturing of offspring, etc.
And all such changes are incremental and the learning involved is invariably by trial and error. And the goals are always short term, probably never met in their entirety, and longer term effects never predictable or even conceivable.
But if there is no such learning, where do all organisms so-called hard wired instinctive tactics come from? The unanswered questions involve the nature of the mechanism, but to me and many others, there’s no question that strategic pressures have taken advantage of such a mechanism to alleviate the inevitable pressures their strategies were self-designed to deal with.
You noted that “In the case of the silver foxes and dogs, changes that affected their ability to produce adrenaline affected their behavior. It wasn’t their behavior that changed their genes.”
Actually it was the survival value placed on those behaviors by the human breeders that changed their genetic structures in unanticipated ways, as the breeders also changed the environments in which those strategies had developed as an adaptive response. Keep the strategies, change the environment, and pressure finds its outlet in physiological change.
And those changes aren’t always beneficial and never completely predictable by the breeders. Who also could not control some of the accompanying changes in the overall behavioral strategy that they had initially been trying to preserve.
You also pointed out that: “Multiple phenotypes can arise from a single change in genotype.”
phenotype |ˈfēnəˌtīp|
noun Biology
the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.
Exactly, and this interaction is always strategic in one form or another.
I note that in the interim between posts you had stated: “Survival is the common thread with all of them mentioned. How they go about doing it is the beauty of genetic diversity. More than one tool can serve to perform the same task.”
But that’s the kind of statement that seems to impart some sort of meaning, but actually tells us nothing about either the cause of the diversity or the nature of how each species deals with it.
The beauty lies in the endlessly complex varieties and permutations of what began eons ago was a fairly simple strategy for survival of what was even then a remarkably complex set of molecules.
And the tool that you mentioned is useless without the strategy that developed it and improved upon itself accordingly.
I wonder what would happen if we applied Occam’s Razor to this discussion.
Anyways, not all adaptations are due to life or extinction pressures. For example, subspecies existing in the same locale. Adaptation to over breed to improve survivability doesn’t require changing a broken strategy, rather, it’s replace the old one with an new and improved one.
There are examples that an evolved species co-exists with its ancestor.
And changes are not all incremental. That’s what the silver fox experiment showed.
Instinct behaviors, although not fully understood, can be linked chemicals such as hormones (adrenaline for fight or flight). Even maternal instinct to rear an infant is linked to signalling molecules. http://www.case.edu/magazine/fallwinter2008/maternalinstinct.html
Not all species survive when challenged with a strong enough pressure. If evolution was strategic, then what will dictate whether one species adapts and another doesn’t? Rather, random changes provides a means to improve the probability it will survive but not guarantee it.
When you say strategic, are you implying that a phenotype must be a logical interaction with the environment?
By the way, I should have caught this earlier. You stated that: “The strategy purpose of all organisms is to survive and reproduce.”
Actually and arguably an organisms only purpose is to obtain and continue to obtain a supply of energy. Reproduction or replication came about as a way to keep that strategy operative. Organisms have no concept of survival or lack thereof. Some gladly die as a way to keep the energy restoration strategy operative through replication.
Others are not all that glad about it, but happiness is an ephemeral goal at best. And then of course they also die.
Again I posted without noting the intervening post. I’m not going to respond to all these arguments, they’re just too superficial.
“Adaptation to over breed to improve survivability doesn’t require changing a broken strategy, rather, it’s replace the old one with an new and improved one.” What the hell is replacement except a change of strategy? Nobody said a strategy has to be broken before an opportunity comes along to improve it in any case.
Of course species can live together. Diverse strategies don’t have to be incompatible and in fact may find some compatibility in that very diversity.
Changes are always incremental. The silver fox experiment showed nothing to the contrary. It in fact was the epitome of an incremental change by way of strategic direction.
And who said a strategy per se will guarantee survival? Strategies account for limited degrees of expected change. They seldom include any vestiges of previously experienced natural disasters, for example.
Adrenaline for flight or fight? That’s one of the proposed initial life preserving strategies. Do you think some learning was not involved in its formulation, and had not contributed to the formation of its mechanistic response functions? God didn’t just zap adrenalin into the system as needed, or did it?
Did that same god just zap in the maternal instinct hormone with no connection to the strategic value of maternal protectiveness?
“Rather, random changes provides a means to improve the probability it will survive but not guarantee it.”
Another essentially meaningless contention. Random change is as much or more the cause of the extinction you mentioned as it is a positive contributor to successful adaptation.
There’s no “logical” interaction with the environment implied here.
Adaptation is not a logical process in any formal sense. Although trial and error is arguably descriptive of biological logic.
Look, you’re way ahead of me in discussing the nature of experimental design. But you’re way behind in understanding the philosophical underpinnings of the science. Go back and study this a bit on your own and then you’ll be prompted to ask a lot better questions.
if you added something else while I was writing this, I apologize in advance for any lack of response.
Yes, well, I’m not well versed on the philosophical underpinnings of the science. But you are lacking in the physical science behind mutations.
As I see it, we are approaching this for two different way. You’re using a top-down approach and I’m using the down-up approach.
I start with the genetic material and work my way up to the organisms phenotype.
First, I’m looking at how mutations occur: point mutations, cross-over events, Viral insertions, hybridization, cross pollination, ect. Next, I look at how gene expression changes: up regulation, down regulation, inactivation, activation, 2ndary structural changes, ect. Equally, I look at how the protein could be affected: product inhibition, fed-back inhibition, enzyme kinetics, temperature, reaction mechanism, binding affinity, tertiary structural changes, ect. Again, one or more mutations are required for these changes and since the causative mutations are random, the changes to the gene expression or protein is also random. I do not differential between single cell organisms, plants and animals since the mechanism for mutations are essentially the same.
So, in my simplistic thinking, the original random mutation event can propagate it’s way through the system and emerges as a change to the phenotype. If the phenotype benefits the organism, what changes is its probability for survival.
Take for example two identical populations, divide them and and place them in identical environments with a selective pressure. There is absolutely no guarantee that they will evolve using the same “strategy”. This was exactly what the citrate consuming E. coli experiment was able to do. Random mutations dictated whether the strain benefited or not.
Phenotype changes are not only incremental (which means 1 step at a time) but also can be a multiplicity. With the silver foxes, the change to adrenaline levels affected several aspects of the phenotype. The foxes that became more tame also exhibited concurrent physical changes: 1) some lost pigmentation 2) the shape of the tail changed 3) the shape of their ears changed, and some with all the changes. All this occurred within 8-10 generations, making it very unlikely it was multiple mutations that occurred at the same time. The behavior and the three physical change occurring simultaneously is what I mean when i say changes are not always incremental, because it wasn’t 1 behavior change but it was 1 behavior change and 3 physical changes (multiplicity, as in 4 changes not just 1).
But you see all you seem to do is observe what happens and apply the most conservative explanations you were taught as explanations for why they happen.
Referring to top-down approach versus down-up, whatever the hell that is, is another way to appear to explain differences in understanding when the approach per se is not the cause of the problem. Approaches to abstract problems are not required to be one-directional. And it’s silly to posit that an approach from any particular direction will by that choice alone inevitably lessen the possibility of a solution, or of a greater overall understanding.
My approach is to look at comparative strategies of organisms at every level and I use the observations of practicing evolutionary biologists to help me in that respect, because I basically am a student, if not a specialist, of and in the motivations and strategies that allow life forms to exist and continue to exist. Both evolutionary philosophy and the aforementioned evolutionary biology are the focus of these studies.
I note for example that you assume an original random causation of a mutation and follow its progress with no thought to the possibility that this progress is both motivated and directed by an algorithmic process in ways which may not only be determinant of that progress, but supply the decision making functions that allow it and its organism to carry out and adapt it’s strategies to its environment and the randomness of events to follow – and as I mentioned before, take advantage, or at least try to, of the opportunities thus presented.
I find this paragraph of yours particularly astonishing:
“I do not differential between single cell organisms, plants and animals since the mechanism for mutations are essentially the same. So, in my simplistic thinking, the original random mutation event can propagate it’s way through the system and emerges as a change to the phenotype. If the phenotype benefits the organism, what changes is its probability for survival.”
Organisms, plants and animals mechanisms for mutation essentially the same? That’s almost insane. For one thing, as the man said, there’s a computer in every living cell (Wetware, Dennis Bray), and those in plants and animals, not to mention fungi and parasites, all operate from a bank of significantly different premises and optional choices.
“If the phenotype benefits the organism, what changes is its probability for survival” That’s very close to a tautological inanity.
Translation: What appears to be beneficial to the organism appears to benefit the organism. Jesus. Have you ever wondered if the changes in the phenotype were in any way due to the choices being made by that organism’s calculative processes? Or did you imagine those processes can only be concerned with the mundane process of a daily feeding of its metaphorical face?
And you still don’t see evidence of any connection between the behavioral changes in the silver foxes that you have obviously noted were concurrent with the physical changes? Amazing.
I have to stop now. I feel a mutation coming on and if I don’t stop, it will carry out it’s mission to protect my brain from the potential damaging effects of incredulity.
who-ah. There is clearly a terminology difference here ’cause how you interpret what I said is not correct, by far.
When I mentioned we are using two different approaches was to say, we are not starting with common assumptions and trying to construct the argument from there. So neither of us will be getting anywhere in convincing each other of whatever. I’m not saying your approach is wrong but rather we are too divergent in our thinking to find a common center point of the argument to work from.
“Have you ever wondered if the changes in the phenotype were in any way due to the choices being made by that organism’s calculative processes?” Nope.
“Or did you imagine those processes can only be concerned with the mundane process of a daily feeding of its metaphorical face?”
That’s too simple. Envision a cell as complex factory, complete with all departments like manufacturing, sales, finance, management, security, ect. How they interact, including human error, red tape, time delays, is how I invision a cell mantains itself and interacts with the work. BUT it’s all based on physical chemical reaction principles.
meant to say… “a cell maintains itself and interacts with it’s environment.” not work.
“And you still don’t see evidence of any connection between the behavioral changes in the silver foxes that you have obviously noted were concurrent with the physical changes? Amazing.”
Sure I have but I may be unsure of what you are trying to say. Here’s a direct behavior and physical appearance connection: Adrenaline affects behavior, a reduction in which made the foxes more tame. Adrenaline is also the chemical precursor from which melanin is made from. Melanin is a dark pigment that gives the silver fox a dark colored coat. A reduction in adrenaline will also cause a reduction in melanin and the reduction manifested as a loss in dark colored fur coats of the foxes.
““If the phenotype benefits the organism, what changes is its probability for survival” That’s very close to a tautological inanity.”
I’m referring to population dynamics.
tucs.fi/publications/attachment.php?fname=TR624.pdf
Specifically, genetic drift: “Most of adaptive dynamics assume that the population is large enough for genetic drift (demographic stochasticity) of the resident strategies to be neglected. New mutants, however, are initially present in a single copy. As it is well known from population genetics, the probability of fixation of a beneficial mutation is less than 1 because it may be lost due to genetic drift (whereas the probability that a deleterious mutation goes to fixation in an (infinitely) large population is zero). To phrase it briefly, a beneficial mutation may invade but not necessarily will invade, whereas deleterious mutations will always go extinct.”
“Have you ever wondered if the changes in the phenotype were in any way due to the choices being made by that organism’s calculative processes? ”
Hmmm. Have you ever wondered if the choices of the organism’s calculative processes are due to changes in the genotype?
No, weing, I haven’t wondered about either, because both choice directed operations are happening all the time.
Draal quoted: ““Most of adaptive dynamics assume that the population is large enough for genetic drift (demographic stochasticity) of the resident strategies to be neglected.”
I presume this refers to mutant strategies replacing resident strategies. You need to ask yourself why this happens and why this, in your view, is not how the organism takes advantage of random opportunities, that advantage being assessed by its calculative apparatus. Then ask yourself what is meant by strategies here and if perhaps this isn’t a reference to behavioral traits, and if this isn’t evidence of behaviors directly effecting physiological changes that go along with genetic drift, etc., etc., etc.
You don’t get what a tautology is either, I presume, which in this present case was saying the same thing twice using different wording as if repetition itself makes either end of the statement true, but only if either part was true to begin with. Nothing in there of course as to how and why the phenotype benefitted the organism.
And contrary to what you contend, cellular operations are NOT “all based on physical chemical reaction principles.” if so, the cell would be and remain being a non-replicable molecular structure.
And adrenaline effects behavior because the strategic process of the particular organism, or superorganism in the case of a fox, uses it as part of its internal signaling apparatus.
Adrenaline, as you seem to infer, does NOT choose strategy. It’s a tactical tool of a strategic plan.
“No, weing, I haven’t wondered about either, because both choice directed operations are happening all the time.”
Any evidence for this?
Read Wetware, A Computer for Every Living Cell, Dennis Bray. He says he has the evidence that them thar things are to blame for just about everthang.
Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are early always derived from empirical observations based on trial and error experimentation.
Aw, snap.
Are you sure you understood him correctly? Choice directed operations are happening all the time. The environment is what rewards or punishes the choices.
Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are early always derived from empirical observations based on trial and error experimentation.
http://www.maths.strath.ac.uk/~caas05/icms/PROTEOMICS.pdf
Weing says: “Are you sure you understood him correctly? Choice directed operations are happening all the time. The environment is what rewards or punishes the choices.”
The environment has a causal relationship to all choice directed activities. It shows us the errors (or at least some of them) in the trial and error process, and new choices are made accordingly. That’s why I’ve made reference to this being an incremental process; regardless of whether the increments come in a group or a series, it’s still incremental. The goals are all short term and in a mechanistic sense, the goal is always to test for an environmental reaction.
As to the paper just submitted by Draal, I’d call it a straw man argument as it addresses claims by others that I have never made, and in fact I’m in general agreement with it. It actually says a lot about the role of strategy, although Draal seems determined to disconsider that aspect of life – too much that he’d have to unlearn perhaps.
Design by trial and error is not related to the one generally described as an anthropomorphic fallacy. We’re not (or I’m not) talking about ascribing human emotions to bacteria (although our emotions are not dissimilar to those of the vertebrate realm – read some Damasio if you’re up to it.). We are however talking about the strategies that all life forms spring from and in that sense have in common. Nobody here was presenting “rational design as an effective research strategy,”
And like it or not all living organism do have goals and purposes. They just don’t know it, since goals and purposes are metaphorical concepts made possible by human levels of abstract thought (some human levels in any case).
(throws hands up) My bad for posting a paper that isn’t so narrowly focused on addressing only your specific point of view. And it was the abstract I posted to give anyone an idea of what the link to the paper was about. It was easier to just post the entire paper than copy and paste every last point against your argument.
One big issue that I have with your idea on strategy is that it’s not testable; specifically, proving all living things have goals and purposes. Additionally, you’d have to also prove alternative possibilities are more likely to be wrong. On the other hand, probability can be modeled and there are a bazzillion models out there. The limitation of a random model is the detail of the information provided; the other technical limitation is there will never be enough computational power to model a complete multicellular organism down to the last atom and electron- we know how to go about it, just not the computing to do it.
The top-down approach can model a macro system quite well by first assigning purpose a network, then to each subnetwork, then to each component. This issue with it is that it can never predict the mechanisms used that make up every part of a system; often there are multiple ways to perform the same task but a global strategy cannot a priori predict the details of the components that gave rise to it.
Conversely, the down-up approach provides a detailed picture of how fundamental laws give rise to a component on a microscale (i.e. the mechanism of an enzyme). What it currently fails miserably at is being able to predict the final function at the macroscale. But the limitation is only the amount of information provided and the ability to crunch the numbers.
From my experience, biologists can’t be arsed to use advanced calculus to solve a problem. (It’s much easier to teach biology to an engineer than it is to teach engineering to a biologist.) I suspect biologist invent these metaphorical strategy concepts to compensate for their inadequacies. It also opens the door for philosophers to wax poetic about life on a limited biological level and gives themselves a sense of worth in the scientific community.
On a historic practical note, a ton more medicines and medicinal practices were discovered by trial and error versus a rational design approach. I’m glad more people don’t think the way you do.
Side note: I also went through Dennis Brey’s journal publications; I’m surprised you never heard of the top-down approach since he uses that term in the title of one of his papers.
Draai writes: “On a historic practical note, a ton more medicines and medicinal practices were discovered by trial and error versus a rational design approach. I’m glad more people don’t think the way you do.”
Why do you persist in misrepresenting what I’ve said? I have never advocated a so-called “rational design” approach. In my last post above I specifically objected as follows: ‘Nobody here was presenting “rational design as an effective research strategy.”’
I was also defending the efficacy of trial and error when I said:
“The environment has a causal relationship to all choice directed activities. It shows us the errors (or at least some of them) in the trial and error process, and new choices are made accordingly.”
That doesn’t mean trial and error is an erroneous methodology. It means trial and error works very well as a biological strategy.
I’m tempted to suspect you are deliberately misrepresenting my words and positions to try to salvage something from your failed arguments. If you are, you should realize that your arguments have still failed.
And of course I know what top down approach is. The point was that since I wasn’t using it, your accusation that such an approach was somehow the cause of our disagreement was just silly. Sticking a label on something to explain it doesn’t mean much if it’s the wrong label. Labeling is also not a substitute for analytical thought.
But you really showed your hand when you wrote this:
“From my experience, biologists can’t be arsed to use advanced calculus to solve a problem. (It’s much easier to teach biology to an engineer than it is to teach engineering to a biologist.) I suspect biologist invent these metaphorical strategy concepts to compensate for their inadequacies. It also opens the door for philosophers to wax poetic about life on a limited biological level and gives themselves a sense of worth in the scientific community.”
Well if, as it seems, you are the engineer here, you are deluding yourself as to how well you’ve absorbed the biological curriculum.
As to philosophers, there would be no science at all without the likes of Aristotle, Hume, etc. And then there’s Darwin, who was nothing if not philosophical about what his observations demonstrated.
Oh, and Leibniz and Newton are both credited with the invention of calculus. Both happened to be renowned, then and now, as philosophers.
Side note: While checking on Bray, did you happen to note he was recently awarded the European Science Prize in Computational Biology?
The problem I’m encountering with reading up on evolutionary biology is that they cannot settle down on the terminology.
You say ‘strategy’ which is an issue ’cause I can’t not find anyone else using the term “strategy”. I’ve seen “rational design strategy” “top down approach” “network biology” “systems biology”, and that’s as close to ‘strategy’ as I could find. If Dennis Brey is tossing it around in his new book “Wetware, …”, then it’s new to his writing. I don’t have access to it without $$ so I intentionally found an article that was free for everyone to read. If ‘strategy’ is the terminology that you bring from philosophy, then it’s no wonder I’m misinterpreting you. So why don’t you spell it out in terms my ignorant self can understand?
Besides, you haven’t correctly reiterated my point of view either and have consistently misinterpreted everything you’ve quoted from me.
That aside, riddle me this: how would you design an experiment that would prove “strategy” is both a means to explain a phenomenon AND predict future observations while disproving the alternative models. That, my friend, is the gold standard I put forward to convince me.
I, myself, already proposed survival of a species (incorporating phenotype, adaptability, genetic drift, ect) is ultimately derived from probability. Probability for one event to randomly occur that follows quantum mechanics and the laws derived therefrom. 1) it’s testable 2) it’s predictive and 3) it’s doesn’t require any unproven assumptions or abstract ideas. It’s already been done for micro systems but the sheer number of atoms in a macro system (for say a fish) makes this impossible to compute fully but the methodology is there.
“Side note: While checking on Bray, did you happen to note he was recently awarded the European Science Prize in Computational Biology?”
Yes, he wrote a computer program to track a E. coli cells moving from a low chemical gradient to a high chemical gradient, that is towards food. It was a stochastic model driven by the probability of protein interactions to explain swimming behavior.
“Well if, as it seems, you are the engineer here, you are deluding yourself as to how well you’ve absorbed the biological curriculum.
As to philosophers, there would be no science at all without the likes of Aristotle, Hume, etc. And then there’s Darwin, who was nothing if not philosophical about what his observations demonstrated.”
I study microbiology, which is outside of my traditional field. Any biologist does not know every aspect of “biology”, starting from DNA and going to social behaviors; we all specialize else no work would get done.
“And then there’s Darwin, who was nothing if not philosophical about what his observations demonstrated.”
In response, here’s the section from the paper I was hoping you would have read:
“Organisms with their adaptations may indeed give the appearance of having been designed and this encouraged the use of the design metaphor when describing evolution by Darwinian natural selection [26, p. 276].
This is somewhat of a paradox since Darwin was responsible for the removal of the mythical figure of the designer or Creator as the agent responsible for the diversity of living forms on our planet. In an attempt to rescue design as an explanatory concept, it has been suggested that it is possible to have a “design without a designer” [27]. Since organisms give the appearance of being designed, this encourages the use of metaphors of goal-directed teleology for describing biological processes in terms of design, purposes, and functions [26].
In reality, a biological function does not entail design for that function and functional descriptions need not be based on psychological notions of design, intention, and purpose [28]. Doing something by design is synonymous to doing it intentionally. It would be more appropriate to say that organisms are fashioned or shaped by selection pressures rather than invoke design and its corollary of intentionality as an explanatory concept.
Many biologists believe that the use of a design terminology is a harmless figure of speech, but others think that it perpetuates the unscientific mental habit of supposing that objects or events have purposes [25]. Attributing a purpose to an object is entirely subjective since purpose has no real existence outside the mind thinking of it. It has been argued that the word function implies a purpose and hinders scientific thinking because it encourages scientists to split any biological entity into sealed compartments with different functions, instead of seeing it as an integrated whole with many connections [25].
Natural selection has replaced the Creator as an explanatory concept although there is in fact no selection, only differential survival. Fitness, which corresponds to anything that increases the chances of survival in a given environment, is often regarded as the basis for selection, although fitness has been described as “another phantom of the human mind” [25]. Fitness is not a property of phenotypes or genes: it is a relation between the organism and the environment.
Today nearly all biologists accept that Darwinian natural selection does not proceed according to the preconceived plan of a designer but that it occurs blindly through the increased survival and reproduction of adaptive random variations. Although the mutations that provide the hereditary variations arise at random, this randomness is counteracted by natural selection which preserves what is useful in their carriers in a given environment and eliminates what is harmful [27]. Darwin’s theory of natural selection provided an explanation for the observed adaptations of organisms and removed the need for an intelligent deity as an explanation for the evolution of life and the emergence of the human species. According to the principles of emergence, the natural world is divided into hierachies that have evolved over evolutionary time [29]. Since blind law is able to explain the diversity of organisms, invoking creationist miracles is no longer necessary and this has put another nail in the coffin of the argument for design [30, p. 265].
According to Dawkins [31, p. 155], accepting Darwinian evolution entails abandoning the human predilection for intentions: “In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky and you would not find any rhyme or reason in it, nor any justice. The universe we observe has precisely the properties we should expect if there is, at the bottom, no design, no purpose, no evil, and no good, nothing but blind pitiless indifference”. Dawkins’ harsh scientific vision, however, does not mean that the potential for morality and ethical behavior in human societies is rendered meaningless and not worthy of serious consideration [30, 35, p.186].”
I appreciate the name dropping but a scientist is not required to be a philosopher to make great breakthroughs in the understanding out Universe. The scientific method is wholly independent of philosophy. Nice try. Here a name for you: Dr. Hahnemann. Without philosophy, we wouldn’t have homeopathy.
http://altmed.creighton.edu/Homeopathy/philosophical.htm
http://www.hpathy.com/philosophy/
http://homeopathy.inbaltimore.org/saine2.html
Or Daniel Palmer and chiropractics.
http://www.spineuniverse.com/displayarticle.php/article812.html
http://www.philosophyofchiropractic.com/
http://chiropracticphilosophyforum.com/
“Well if, as it seems, you are the engineer here, you are deluding yourself as to how well you’ve absorbed the biological curriculum.
As to philosophers, there would be no science at all without the likes of Aristotle, Hume, etc. And then there’s Darwin, who was nothing if not philosophical about what his observations demonstrated.”
I study microbiology, which is outside of my traditional field. Any biologist does not know every aspect of “biology”, starting from DNA and going to social behaviors; we all specialize else no work would get done.
“And then there’s Darwin, who was nothing if not philosophical about what his observations demonstrated.”
In response, here’s the section from the paper I was hoping you would have read:
“Organisms with their adaptations may indeed give the appearance of having been designed and this encouraged the use of the design metaphor when describing evolution by Darwinian natural selection [26, p. 276].
This is somewhat of a paradox since Darwin was responsible for the removal of the mythical figure of the designer or Creator as the agent responsible for the diversity of living forms on our planet. In an attempt to rescue design as an explanatory concept, it has been suggested that it is possible to have a “design without a designer” [27]. Since organisms give the appearance of being designed, this encourages the use of metaphors of goal-directed teleology for describing biological processes in terms of design, purposes, and functions [26].
In reality, a biological function does not entail design for that function and functional descriptions need not be based on psychological notions of design, intention, and purpose [28]. Doing something by design is synonymous to doing it intentionally. It would be more appropriate to say that organisms are fashioned or shaped by selection pressures rather than invoke design and its corollary of intentionality as an explanatory concept.
Many biologists believe that the use of a design terminology is a harmless figure of speech, but others think that it perpetuates the unscientific mental habit of supposing that objects or events have purposes [25]. Attributing a purpose to an object is entirely subjective since purpose has no real existence outside the mind thinking of it. It has been argued that the word function implies a purpose and hinders scientific thinking because it encourages scientists to split any biological entity into sealed compartments with different functions, instead of seeing it as an integrated whole with many connections [25].
Natural selection has replaced the Creator as an explanatory concept although there is in fact no selection, only differential survival. Fitness, which corresponds to anything that increases the chances of survival in a given environment, is often regarded as the basis for selection, although fitness has been described as “another phantom of the human mind” [25]. Fitness is not a property of phenotypes or genes: it is a relation between the organism and the environment.
Today nearly all biologists accept that Darwinian natural selection does not proceed according to the preconceived plan of a designer but that it occurs blindly through the increased survival and reproduction of adaptive random variations. Although the mutations that provide the hereditary variations arise at random, this randomness is counteracted by natural selection which preserves what is useful in their carriers in a given environment and eliminates what is harmful [27]. Darwin’s theory of natural selection provided an explanation for the observed adaptations of organisms and removed the need for an intelligent deity as an explanation for the evolution of life and the emergence of the human species. According to the principles of emergence, the natural world is divided into hierachies that have evolved over evolutionary time [29]. Since blind law is able to explain the diversity of organisms, invoking creationist miracles is no longer necessary and this has put another nail in the coffin of the argument for design [30, p. 265].
According to Dawkins [31, p. 155], accepting Darwinian evolution entails abandoning the human predilection for intentions: “In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky and you would not find any rhyme or reason in it, nor any justice. The universe we observe has precisely the properties we should expect if there is, at the bottom, no design, no purpose, no evil, and no good, nothing but blind pitiless indifference”. Dawkins’ harsh scientific vision, however, does not mean that the potential for morality and ethical behavior in human societies is rendered meaningless and not worthy of serious consideration [30, 35, p.186].”
I appreciate the name dropping but a scientist is not required to be a philosopher to make great breakthroughs in the understanding out Universe. The scientific method is wholly independent of philosophy. Nice try. Here a name for you: Dr. Hahnemann. Without philosophy, we wouldn’t have homeopathy.
altmed.creighton.edu/Homeopathy/philosophical.htm
http://www.hpathy.com/philosophy/
homeopathy.inbaltimore.org/saine2.html
Or Daniel Palmer and chiropractics.
http://www.philosophyofchiropractic.com/
chiropracticphilosophyforum.com/
Draal, you say you can’t find anyone else using the term strategy? This in spite of the fact that you used it when you stated early on: “The strategy purpose of all organisms is to survive and reproduce.”
Of course you were wrong, but at that time you seemed to believe in both strategy and purpose.
But just to get you back to that other frame in your mind, check this out: http://www.cambridge.org/resources/0521674557/4836_Appendix%20Rohde.doc.
Plenty of good stuff about strategy there from those unscientific biologist blokes.
Also what you give as the gold standard of proof shows you misunderstand (perhaps with a purpose) the concept of falsifiability, which does not require the disproof of alternate models (this isn’t about engineering). Here’s a clue as to why: Your standard would require the disproof of creationism which is craftily fashioned so as not to be falsifiable. Are you a closet creationist perhaps? That would be consistent with the way you put forward this specious argumentation.
In any case the concept of life as a strategic entity is at this point in history virtually a part of the definition that separates life from non-life, and even with that the line isn’t clear – whether viruses have viable strategies because they are not self-replicating is to some an unsettled question. (You see this is because strategy infers that there’s a choice making apparatus behind it, and some say viruses don’t have one – although Bray would say they do.)
So I don’t need to design any fresh experiment to prove that life is a strategic entity. Darwin already did that as have countless others. If you don’t believe them, you won’t believe me.
And Bray wasn’t just explaining E.coli swimming behavior as a function of protein interactions. Jesus Christ on your quantum mechanical crutch. He was demonstrating their computational functions, and relating this to their adaptability, responsiveness, and intelligence. Yes, the intelligence that is there for no other purpose than to strategize.
I hadn’t noticed that intervening post, but since I never ascribed any purpose to life except that of getting and remaining fed, there’s no reason to comment except to reiterate that biological designs are not goal oriented. They are the workable results of trial and error efforts at solving incremental problems.
Oh yeah, you said, “The scientific method is wholly independent of philosophy.” What are you, still in high school? That’s just dumb.
I forgot to add that this (from your unattributed paper) seems to be the conservative view of mutations that you may be using to support your bias against early life forms having any intelligent effect on their evolution.
“Although the mutations that provide the hereditary variations arise at random, this randomness is counteracted by natural selection which preserves what is useful in their carriers in a given environment and eliminates what is harmful [27].”
I guess that guy (probably some sort of systems biologist) never heard of genetic parasites, just to give one example of non-random mutation effectors – both as to their hosts as well as themselves.
Oh and methinks you’re spending too much time with your sonic spear.
“The environment has a causal relationship to all choice directed activities. It shows us the errors (or at least some of them) in the trial and error process, and new choices are made accordingly.”
Who makes these “new choices”? I would think that the organisms programmed with the other choices are now out of the picture. If the “new choices” are variations in the programs of the descendants of organisms that survived, then I can follow it.
I’ve had time to reflect a bit and have concluded I should not post on blogs after a night of drinking. Secondly, you’ve made me realize I generally, um, don’t know what I’m talking about when it comes to philosophy. My jabs at philosophy were sophomoric and uninformed. If philosophy is the process of reasoning, then science necessitates reasoning to explain observations, and hence requires philosophy. I artificially assumed that since philosophy does not require experimentation to empirical proof, than science does not require philosophy.
“Draal, you say you can’t find anyone else using the term strategy? This in spite of the fact that you used it when you stated early on: “The strategy purpose of all organisms is to survive and reproduce.”Of course you were wrong, but at that time you seemed to believe in both strategy and purpose.” Poor choice of words upon reflection. I still stand by that the goal of an organism is to survive and reproduce. But I don’t attribute the necessity of a strategy to achieve that goal.
“Also what you give as the gold standard of proof shows you misunderstand (perhaps with a purpose) the concept of falsifiability, which does not require the disproof of alternate models (this isn’t about engineering). Here’s a clue as to why: Your standard would require the disproof of creationism which is craftily fashioned so as not to be falsifiable. Are you a closet creationist perhaps? That would be consistent with the way you put forward this specious argumentation.”
Right, so, I didn’t argue this correctly since I injected a dichotomy criterion but you missed (or ignored) the point. Let’s replace proof and disproof with more likely and less likely. Part of proving a hypothesis is more likely to be correct (since absolute proof is unattainable) is to also show that the most relevant alternative hypothesis are not as plausible (since absolute falsifiability is unattainable). In addition, for a hypothesis to be more likely, it also needs to be able to predict future observations. Assigning a strategy to functions explains the goal of an organism very nicely but it fails to be predictive. When challenged with a selective pressure you’re unable to predict how an organism will evolve. Your idea is untestable and will remain as an abstract concept.
“Closest creationist” Ahhhhh. One hell of a solid argument you made there to equate A to B to C to closest creationist.
“So I don’t need to design any fresh experiment to prove that life is a strategic entity. Darwin already did that as have countless others. If you don’t believe them, you won’t believe me.” Darwin’s observations decoupled the necessity for a higher power to be driving evolution “but that it occurs blindly through the increased survival and reproduction of adaptive random variations.”
“Oh yeah, you said, “The scientific method is wholly independent of philosophy.” What are you, still in high school? That’s just dumb.”
Point taken. I did a little reading on the intertubes and I agree that my statement is utter rubbish.
“In any case the concept of life as a strategic entity is at this point in history virtually a part of the definition that separates life from non-life, and even with that the line isn’t clear – whether viruses have viable strategies because they are not self-replicating is to some an unsettled question. (You see this is because strategy infers that there’s a choice making apparatus behind it, and some say viruses don’t have one – although Bray would say they do.)”
And where do you make the demarcation of when non-living material first became alive? 4+ billion years ago, the Earth was void of life (yes?). Non-living material does not have a strategy (yes?). At some point, the first single-cell organism emerged (yes?). How then did the strategy of life materialize from non-living material? I propose that it was just a matter of probability for all the events to occur to give rise to a cell.
“(from your unattributed paper)” –see the link to the article I posted above.
“I guess that guy (probably some sort of systems biologist) never heard of genetic parasites, just to give one example of non-random mutation effectors – both as to their hosts as well as themselves.”
Here’s the thing. A mutation by a genetic parasite is possible but not a given. Person A carries a virus and Person B does not. Person B would need to intersect spatially within 72 hours (given that the virus is only viable on a door handle or whatever for 3 days) the path of Person A. Or, Person A would need to infect Person C who in turn infects Person B. Even if Person B is exposed to the virus, the immune system can destroy the virus before it enters a host cell. Even if the virus infects a cell, the cell has the ability to destroy the virus DNA before it integrates into the genome. What I’m saying is that for each event to occur there is a probability that the infection process can be terminated before completion. In other words, the existence of a virus does not necessity for a mutation to occur but provides the probability for it to occur.
“Oh and methinks you’re spending too much time with your sonic spear.”
Me thinks you play WoW too much to know what a sonic spear is; I had to look it up. Me thinks I would have appreciated a sonic screwdriver reference (Dr. Who) but me unsure of what the hell you are implying. Went over my head.
“Jesus” … “Jesus Christ” Me thinks you use the Lord’s name in vain too much and he will smite you. You just wait, He’s a cooking something good for you.
“Jesus Christ on your quantum mechanical crutch.” Ever hear of the Heisenberg uncertainty principle? I’m trying to explain little by little where randomness ultimately arises from.
And one last thing, before you chalk up a win in your score book, “The weakness of my argument does not imply the strength of yours” – Sigmund Freud. I admittedly have a long way (a very long way) to presenting an coherent argument so it does me no good when you just dismiss any point you disagree with by just saying I’m just wrong and move on.
One last thing, what is wrong with randomness and probability giving rise to the number of permutations that result in evolution? All I’ve heard from you is why strategy is the answer in support of your argument but I can’t take you to task against your reasoning to why it’s wrong since you’re more preoccupied with deconstructing my tangential rantings.
here’s another misinformed view you hold of what I’ve said:
“Organisms, plants and animals mechanisms for mutation essentially the same? That’s almost insane. For one thing, as the man said, there’s a computer in every living cell (Wetware, Dennis Bray), and those in plants and animals, not to mention fungi and parasites, all operate from a bank of significantly different premises and optional choices.”
Are you aware of the Central dogma of molecular biology; DNA encodes for RNA which encodes for proteins?
en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
Funny how bacteria, fungi, plants and animals all operate this way. DNA is DNA and how it’s manipulated is not exclusive to one Kingdom. For example, radiation entering a plant cell and damaging its DNA is going to be an identical process if it was to happen to an insect cell. Another example, DNA polymerase is inherently prone to errors and gives rise to point mutations. A DNA polymerase makes mistake in an identical manner in a yeast cell as say a chicken cell. Even viruses infect bacteria and insert viral DNA into a genome; it’s not just animals that suffer from “colds”. You clear on what I’ve said now? Far from being insane.
Draal, in the context we were discussing, dismissing the importance of strategy by saying all mechanisms for mutation are essentially the same may not be insane, but goofy it surely was. All have DNA yet all have evolved in radically different ways. Randomness doesn’t explain either how or why. But taking ADVANTAGE of randomness by the other thing these life forms had and have in common, which is a basic strategy of assessment of choices through trial and error, begins the explanatory process. (Explanations then differing in quality according to the nature of the curiosity that calls them into question.)
Even minute differences in surrounding circumstances make differences in the evolution that results predictable. But it’s the difference that is predictable, not the precise results. And here’s the kicker: DNA that pops or has popped into being randomly and exercises no strategic potential will predictably not evolve at all, because replication is a strategic process. That’s the first step we need to take in understanding how life not just came about, but how it has been permitted to evolve in what most likely IS a random and indeterminate universe.
So where did the strategic potential come from that makes DNA common to life, you ask? That’s the question for which we as yet have no widely acceptable answer. We have a number of hypotheses in the process of being tested, but for now, no evidence except our assessment of their logical probabilities.
My view is that DNA is in and of itself a strategic construct. Chances are that there are a myriad of such constructs in nature, and ours is the one particularly suited to earth. But now I’m getting too close to philosophizing for your taste so I’ll leave it at that.
Weing, you stated: “If the “new choices” are variations in the programs of the descendants of organisms that survived, then I can follow it.” Yes, that’s what it comes down to, the question then being how exactly did the variations get there. Were they in any sense directed, or in every sense due to random mutation, and if the former, how far does that go? I don’t know, but we’re working on it.
“Draal, in the context we were discussing, dismissing the importance of strategy by saying all mechanisms for mutation are essentially the same may not be insane, but goofy it surely was.”
I don’t know what would make you think that it’s not goofy ‘cept if you took a microbio class I guess. Fun facts: Homo sapien DNA polymerase alpha subunit shares 98% protein identity to a recces monkey, 91% to cattle, 88% protein identity to a Chinese rat, and 84% to a dog. That some awfully conserved protein sequences for being so different types of animals.
“Randomness doesn’t explain either how or why. ”
Randomness allows for all possible outcomes and probability adds weight to one outcome over another. For instance, an individual is born with a beneficial mutation. There is no guarantee that his offspring will carry the mutation if we follow Mendelian genetics. Basically, better luck next time. But if it is passed down, then his offspring have a probability advantage in survival. No strategy is necessary. And negative mutations necessarily will be removed from the gene pool overtime.
So, the ‘how’ is: every event is represented but only a few are tested at any given time but given enough time, all events will arise; it’s just that different events can result in the same outcome (i.e. multiple tools do the same job) so not all possibilities need to be tested to find the ‘best’ one.
And the “why”: Randomness is inherent to the Universe. Quantum mechanics is example (oh, no, he went there again!), or more simply, flipping a coin or more aptly, a loaded die. It’s a known mechanism for change. Occam’s razor would preferentially choose the model with the least # of new assumptions (here’s a slippery slope for me so I’m hesitant to use it but it’s sooooo appealing). Randomness isn’t an assumption, it’s reality. No new ideas are necessary. Strategy is an assumption that a choice is being made. Therefore, Occam’s razor prefers the model with no new assumptions. NOTE: This isn’t a proof of either model being correct or incorrect, just a tool to discern which one is more likely than another; it’s also possible Occam’s razor is completely inappropriate for complex systems like evolution so I take this reasoning with a grain of salt.
Randomness is quite testable and predictive. Say you have a loaded die but you don’t know which number is favored. By rolling the die a bunch a times, you can statistically prove what the weighted number is (that is you know the function of the die is to prefer one outcome over another). Now, if you where to take that die to the casino and had one chance to roll it and bet on the number to win big $$ (or quid), What number would you pick? You may say, it’s ‘strategy’ to pick the weighted number. But there’s no other winning ‘strategy’ to choose from. If you could return every day with more cash to bet and roll your die, you’d still pick the weighted number because probability dictates that over time, the weighted number will win out. You may call that a strategy. But, if you were to repeat this experiment numerous times, is there any better ‘strategy’ to choose from to consistently win? No. And therefore, it’s no strategy at all since no other choice is needed to succeed.
Ow, that made my head hurt.
Your head should hurt, because what randomness predicts is that without the power of choice, all one can predict is predictability itself. In fact without the mechanism of choice, predicability would be a concept devoid of an executive process.
That’s rubbish. Probability will result in a distribution of events occurring at a predefined frequency. You don’t “choose” to have a coin land on heads or tails.
I should have said, “A coin doesn’t “choose” to land on heads to tails.
That’s right, a coin being tossed has no choice. It can exercise no options. It can’t calculate and thus has no executive function that such ability would require. It never will unless you make coins out of strategic constructs – DNA as a bankable item perhaps.
You may be having some problems with the level of abstraction you’re used to operating on. There’s a bit of a paradox here for example. The fact that the predictable result of coin tossing over time will virtually always be the same, yet remain at best uncertain, shows that all you have predicted is the nature of predictability. There can be no prediction that the coin itself will ever attain the facility to predict even its immediate future in the tossing process. Worse, nothing seems to be there to make a prediction about anything at all, yet the concept of predictability still floats there in its platonic realm.
Draal wrote: “Randomness allows for all possible outcomes and probability adds weight to one outcome over another. For instance, an individual is born with a beneficial mutation. There is no guarantee that his offspring will carry the mutation if we follow Mendelian genetics. Basically, better luck next time. But if it is passed down, then his offspring have a probability advantage in survival. No strategy is necessary. And negative mutations necessarily will be removed from the gene pool overtime.”
Enough of this nonsense about the ubiquity of randomness, which to begin with is a purely theoretical, if not tenuous, proposition, as all evidence about the nature of causation, and the seeming immutability of the physical laws of nature, etc., convinces many there may be no such thing as randomness. So to preserve the concept for the sake of evolution, it’s been limited to the proposal that mutations were accidental in the sense they weren’t chosen by the organisms, any more than they have chosen the wind to blow or the sun to shine. What they are also presuming by the use of random and accidental is that selection was and is undirected.
But note that even so, the organisms have somehow “learned” to protect themselves from the wind and the sun, as well as take full advantage of them as sources of energy. Draal might then “choose” to argue these advantages were not taken by any form of choice, either by the forces involved or by these organisms (choice being the essential element of strategy of course).
But if that silliness were so, every action taken by a plant or animal would have to be purely reactive, and since these acts seem to be beneficial and constructive, life forms having flourished, some choice must have been made somewhere in the universe in the distant past to make this beneficial behavior a relatively consistent success over the earth’s evolutionary history. Which, on the assumption that randomness can exist, pretty well would reduce its extent in the present to the barest minimum. And would mean that the universe was essentially deterministic, and not only that, all events and behaviors virtually predetermined, Pretty much signaling the end of randomness as we know it.
So if, as Draal contends, mutations are indeed the result of undirected accident, the natural selection theory provides that some mechanisms are selecting in the beneficial, and selecting out the negative. These somethings are nevertheless choice making processes. Either the organism is in some way directing the choices, or nature has made the choices for it somewhere down the trail of causation – although in the end, the mechanism will have to operate with the organism’s cooperation.
Thus even if the mutation is not forced, or specifically directed or engineered, or even predetermined, there was at least some choice involved in the selection. Draal and his like say, “no strategy is necessary.” But this element of choice tells us some selective strategy has to be kicking in somewhere very close to home.
heh. you can’t let this one go.
“Enough of this nonsense about the ubiquity of randomness, which to begin with is a purely theoretical, if not tenuous, proposition, as all evidence about the nature of causation, and the seeming immutability of the physical laws of nature, etc., convinces many there may be no such thing as randomness.”
Physical laws of nature indeed. Heisenburg’s Uncertainty Principle? Quantum tunnelling? Just because you are ignorant of more advanced physics does not necessitate it is purely theoretical. Nice little logical fallacy.
“So to preserve the concept for the sake of evolution, it’s been limited to the proposal that mutations were accidental in the sense they weren’t chosen by the organisms, any more than they have chosen the wind to blow or the sun to shine.”
Funny how the mechanisms for mutations to occur are known and can be reproduced in a lab. The frequency of the occurrence of mutations will follow a probability distribution.
“So if, as Draal contends, mutations are indeed the result of undirected accident, the natural selection theory provides that some mechanisms are selecting in the beneficial, and selecting out the negative. These somethings are nevertheless choice making processes.” heh. Again, a probability distribution will direct positive mutations to succeed and negative mutations to cease, over a long enough time scale, and the age of the Earth is plenty long. As the saying goes, Even a blind squirrel can find a nut.
“Which, on the assumption that randomness can exist, pretty well would reduce its extent in the present to the barest minimum. And would mean that the universe was essentially deterministic, and not only that, all events and behaviors virtually predetermined, Pretty much signaling the end of randomness as we know it.”
Again, your ignorance of advanced physics and statistics is apparent.
If you are willing to hear other voices, listen to SGU #204, (starting 28:15). In short, “Genes don’t want anything.” -Rebbecca Watson
Dr. N knows everything. I believe in Dr. N. We all must worship Dr. N.
Draal, you poor fellow,
Randomness according to Heisenburg’s Uncertainty Principle is NOT pervasive. To attribute it as you do to as being nature’s default decision making process makes me more than suspect I understand advanced physics much better than you do. And the uncertainty principle in fact allows for the consideration that we have the will to make decisions – that contrary to your contentions, they need NOT be made by what you want to see as “a probability distribution [that] will direct positive mutations to succeed and negative mutations to cease, over a long enough time scale” The uncertainty principal supports the argument for the exact opposite.
“Even a blind squirrel can find a nut” only means it can get lucky. Which does come down to the essence of your world view, that everything happens because luck is statistically on our side.
The probability distributions that show show a frequency of mutation in some of these lab simulations don’t show anything about HOW or WHY they are selected by living organisms, now do they.
And if you look, you’ll find many who object to the procedures as garbage in garbage out, as they tend to reflect confirmation bias in the researchers and in no way are predictive of evolutionary results in the real world.
Show me one that actually showed how a present day form will then be found after the study to have “mutated” in the intervening future. You can’t do that without rigging the data and you know it (or actually it would seem that you don’t).
And you completely miss the point that if, as you believe, there is no strategy involved in evolution of life, that even with randomness, it would have to be at a bare minimum to make your theory work – simply because if you deny choice in the present, your probability theory is a version of determinism in nature, and if you accept that some choice must at least have been made in the distant past, the present, without the need of choice, is still effectively deterministic – and randomness, as Heisenberg actually posits, is necessarily minimal.
Do you really think that Dr. N or Rebecca Watson support you belief that nothing at all about evolution is directed, or that strategy plays no part in the evolutionary process? They simply don’t.
“Draal, you poor fellow,
Randomness according to Heisenburg’s Uncertainty Principle is NOT pervasive. To attribute it as you do to as being nature’s default decision making process makes me more than suspect I understand advanced physics much better than you do.”
ROFLMAO. It was just ONE example that randomness is inherent to the Universe (since it’s fundamental to every single electron in the whole wide Universe) since you denied physical laws have randomness as part of their theory. I never said it was the ONLY reason for randomness in the Universe.
“Do you really think that Dr. N or Rebecca Watson support you belief that nothing at all about evolution is directed, or that strategy plays no part in the evolutionary process? They simply don’t.”
Dr. N said the predominant view of evolution is not deterministic but he didn’t discount other forces playing minor roles. THAT’s his view, in black and white ink. I just accept the majority view as, well, the most probable.
This blog is not an appropriate place to school you on advanced physics so forgive me for not going into depth on every example I provide.
I agree with Draal. Choice is just an illusion. As a donkey once said “I can bite or I can chew.” Ever wonder if your view of randomness is possibly skewed? Didn’t Poincare discover deterministic chaos in his solution to the three body problem? It’s been a while since I studied physics, but I thought the uncertainty principle meant that you cannot simultaneously know the position of an electron if you know its precise momentum and vice-versa.
Draal,
Talk about a laugh, you back off on the philosophical import of the Heisenburg principle, and then basically lie when you say I denied physical laws have randomness as part of their theory. I said clearly that others deny that the sort of randomness dealt with by Heisenburg exists in nature. I hold with Heisenburg that physical laws are reliably predictive, but the inevitability of the causative process in nature is not certain.
You seem not to know about the ongoing controversy as these matters apply to free will or the lack thereof. Your knowledge of causality theory in general is worse than even the folk wisdom variety.
If Dr. N said the predominant view of evolution is not deterministic, then he doesn’t support your contrary views to that effect, now does he? Just admit it and stop the blind squirrelly attempts to get around it. if that’s the majority view, you still have shown no indication that you accept it. Majority view being as a rule a fairly dumb position to take as either a skeptic or a scientist, but then you’re not really a scientist, are you?
Incidentally, as to the last comment, neither you or your examples would appear to have any depth that could be gone into.
Weing, tell us what your view of the principle in question has to do with evolution?
And for choice to be an illusion, one would still have to go through the motions of making it.
And deterministic chaos is about the vast web of causality, unpredictable at the outset, yet at the same time inevitable as to the nature of its consequences. A bit like Dennett’s idea of compatibilism.
Draal on the other hand is a determinist. Apparently you are as well.
I suppose that Donkey was also. They do tend to come in threes.
“Show me one that actually showed how a present day form will then be found after the study to have “mutated” in the intervening future. You can’t do that without rigging the data and you know it (or actually it would seem that you don’t).”
Title: CHROMOSOMAL MUTATION FOR CITRATE UTILIZATION BY ESCHERICHIA-COLI K-12
Author(s): HALL, BG
Source: JOURNAL OF BACTERIOLOGY Volume: 151 Issue: 1 Pages: 269-273 Published: 1982
Title: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
Author(s): Blount ZD, Borland CZ, Lenski RESource: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 105 Issue: 23 Pages: 7899-7906 Published: JUN 10 2008
Title: The rate at which asexual populations cross fitness valleys
Author(s): Weissman DB, Desai MM, Fisher DS, et al.Source: THEORETICAL POPULATION BIOLOGY Volume: 75 Issue: 4 Special Issue: Sp. Iss. SI Pages: 286-300 Published: JUN 2009
Title: Accumulation of mutants in “aging” bacterial colonies is due to growth under selection, not stress-induced mutagenesis
Author(s): Wrande M, Roth JR, Hughes DSource: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 105 Issue: 33 Pages: 11863-11868 Published: AUG 19 2008
Science. 2003 Jan 24;299(5606):555-8.
Title: Ohno’s dilemma: Evolution of new genes under continuous selection
Author(s): Bergthorsson U, Andersson DI, Roth JRSource: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 104 Issue: 43 Pages: 17004-17009 Published: OCT 23 2007
Title: Ohno’s Model Revisited: Measuring the Frequency of Potentially Adaptive Mutations under Various Mutational Drifts
Author(s): Bershtein S, Tawfik DSSource: MOLECULAR BIOLOGY AND EVOLUTION Volume: 25 Issue: 11 Pages: 2311-2318 Published: NOV 2008
and a review:
rothlab.ucdavis.edu/publications/OriginMutations-2006.pdf
“you back off on the philosophical import of the Heisenburg principle” Um, my original point was that randomness arises from quantum mechanics. You called it a crutch so I thought giving the Uncertainty Principle as an example that I figured you’d be able to understand a small part of quantum mechanics on at least some level. I’m not backing off the importance, it’s just not useful to continue to talk to you about it since you obvious have no understanding of how the formulas are derived but rather you go for the over simplified explanations you’ve found from google. I said that quantum mechanic necessitate randomness and that randomness propagates through the whole system.
“then basically lie when you say I denied physical laws have randomness as part of their theory. ”
—
“Enough of this nonsense about the ubiquity of randomness, which to begin with is a purely theoretical, if not tenuous, proposition, as all evidence about the nature of causation, and the seeming immutability of the physical laws of nature, etc., convinces many there may be no such thing as randomness.”
My bad for thinking you held this view too. But an atomic property is universal. so ROFLMAOCOPTERLOL.
“You seem not to know about the ongoing controversy as these matters apply to free will or the lack thereof. Your knowledge of causality theory in general is worse than even the folk wisdom variety.” Yet another Ad hominem logical fallacy.
“Majority view being as a rule a fairly dumb position to take as either a skeptic or a scientist, but then you’re not really a scientist, are you?” You really like using the Ad hominem logical fallacy. Grow up. I agree with the majority because I personally believe it the most probable mechanism for evolution, not because a bunch of people agree on something. (Great men think alike)
“If Dr. N said the predominant view of evolution is not deterministic, then he doesn’t support your contrary views to that effect, now does he? Just admit it and stop the blind squirrelly attempts to get around it. ”
If I misrepresented his view, here it is again “even if it were true that in some cases mutations are triggered by environmental stress, that still would not make it the dominant mode in evolutionary change, nor would it mean that random mutations followed by selection would not work, as you seem to indicate above.”
Evolution is not “deterministic” in the path it takes as your Your “choice” hypothesis implies that the organism already has a set of tools to choose from to evolve and picks one.
Rather, Nature has a whole bunch of ways to elicit mutations but one event is more likely than others, hence randomness and probability– a successful outcome is not guaranteed.
If an organism has a choice to adapt or not, shouldn’t it adapt every time? Obviously it doesn’t as species go extinct all the time.
“It’s been a while since I studied physics, but I thought the uncertainty principle meant that you cannot simultaneously know the position of an electron if you know its precise momentum and vice-versa.”
That’s correct but Artie missed the point that randomness is omnipresent and got hung up on what essentially is a rounding error. How can such a small variation make any such difference if the magnitude is so small compared to the rest of the system?
Take temperature for example. By definition, it’s the average of the velocities of the atoms in the system, from slow moving to very fast moving. A binary chemical reaction depends on the probability that two atoms or molecules are traveling at the right velocity, direction and orientation. If a reaction has a high activation energy, raising the temperature increases the odds that two atoms smack into each other with enough energy, and the increased velocity dictates that the number of collisions will increase. And at the atomic level, the magnitude of the Uncertainty Principle is relevant and can effect a binary event like a chemical reaction. Artie has a mental block from accepting that tiny numbers have any relevance at the macroscopic level.
Let’s see, too many targets, must shoot at random. Saying your position i wrong is not ad hominem. Saying you’re not a scientist isn’t either if it’s true and tends to excuse your ignorance. (You don’t even know what the fallacy consists of, do you?)
Those examples you give only show that the mutation theory likely holds up as far as criticism of the effectiveness of the mechanism apply. To the extent that they are predictive they support my views rather than yours.. I have three books right in front of me that tell us more about e.coli than you have to offer in those examples. It’s more and more obvious that you don’t have any idea what any of these papers really mean.
Of course you don’t, you’re not a scientist. You thought you could pull off the pretense, but you really can’t, you know. Not even close. You have no lab and you have no colleagues. if you did, you know they’d laugh you out of the building if they knew your views.
Talk about Googling, you do it and have no idea what the stuff really means, and then you see evidence there that I’m correct and accuse me of going there for the idea.
Almost everything I’ve said is based on my own research. Google is nevertheless valuable for all of us, as it’s like having a library in your lap – you do believe in reading books – or do you? I have the hard copy of Wetware – something that anyone pretending to know the computational aspects of biology wasn’t even aware existed – and couldn’t even understand the reviews, excerpts, etc..
You admit you know little about philosophy, and yet you think you can freely apply principles of scientific philosophers such as Heisenburg with only a superficial idea of what he’s all about. Tell me again that he supports your version of determinism, and how. Except the hows and whys of things seem to be outside the reach, or maybe its just the grasp, of your curiosity.
You proudly repeat: “I said that quantum mechanic necessitate randomness and that randomness propagates through the whole system.” You don’t even know what that means, do you, because it certainly has nothing to do with your deterministic theory of choiceless evolutionary progress. (Perhaps you’re into choiceless awareness meditation which arises most prominently from the Theravadan tradition – according to Googlismic science.)
An atomic property is universal? Sounds like Liebniz view of monads. Oh yeah the philosopher dude that invented the calculus.
He must be right, even if monads went out of fashion.
Oh and again, random mutations followed by selection, as I demonstrated are NOT a way to bypass choice, because selection means choosing, you non-scientist, non-philosopher, non epistemologist you.
“Your “choice” hypothesis implies that the organism already has a set of tools to choose from to evolve and picks one.” No, doofus, it means it participates in the in and out mutation selection process that you support, but believe is predetermined by the universality of the atom.
Seriously, look at this last sentence of yours:
“If an organism has a choice to adapt or not, shouldn’t it adapt every time? Obviously it doesn’t as species go extinct all the time.”
You should make that your epitaph if that’s the best you can come up with..
“Draal on the other hand is a determinist. Apparently you are as well.”
Exactly how does randomness equate deterministic? If an organism has a choice, isn’t that deterministic, since it determines it’s fate?
Way back when, I said that if you could model a system in a computer down to the last atom, you could calculate the outcome. Which outcome is determined is random though, because the interactions between components are subject to probability. This necessitates running the model a bunch of times to determine the system’s probability distribution. With the probability known, I can guess what the the outcome of the next computer run will be but it does not guarantee I’ll be right but I’ll be right most of the time. What makes a system appear to be deterministic is that in reality, a certain event is much more likely to occur than others. Over short periods of time, the model appears to only have one solution. However, over a long enough time frame (say, half age of the Earth), different solutions will emerge. Many of them will have followed the same path for a while before branching off.
There is no necessary input of “choice”. If it was true, a “choice” would have been necessary for life to emerge from the primordial ooze. And the answer is 42.
“Let’s see, too many targets, must shoot at random. Saying your position i wrong is not ad hominem. Saying you’re not a scientist isn’t either if it’s true and tends to excuse your ignorance. (You don’t even know what the fallacy consists of, do you?)”
Ad hominem
An ad hominem argument is any that attempts to counter anothers claims or conclusions by attacking the person, rather than addressing the argument itself.
You’ve repeatedly intentionally injected inflammatory remarks. So, I’d say I nailed it pretty solidly.
Its obvious you are more interested in being an ass so let agree to disagree.
I forgive you none the less.
If the person pretends to be knowledgeable, and uses that pretense to advance otherwise unsupportable dicta, its within the dictates of logic to attack the source of the pretense.
“There is no necessary input of “choice”. If it was true, a “choice” would have been necessary for life to emerge from the primordial ooze.”
It WAS necessary. For example, the initial forms had to learn to seek out energy. They would have learned by happy accident that their first acceptance of energy was something that bore repeating, and they “chose” to do so. When its energy source inevitably waned, the organism had to have “learned” that choices were needed to search out more or receive equivalent energy from a different source.
This is a scientifically plausible hypothesis which can and has been and will continue to be subject to scientific tests.
You might find something like it in Google although I doubt it. You’d have to put it together, and couldn’t unless you understood what you were doing.
Methinks you are anthropomorphisising, whether there is or is not such a word. It’s your choice.
Can you give a quote from Wetware that supports your interpretation? If you can, I’ll write to him to clarify.
Weing,
I didn’t get that from Wetware. It’s related to what I mentioned to you that we (including me) have been working on for some time now. But Bray does talk about the learning abilities of the most primitive or basic life forms and their calculative and choice making processes. As do others.
In my view, what people like to call anthropomorphizing is largely or at least often based on our cultural misunderstanding of the progressive nature of the evolutionary process – the feeling that non-humans supposedly ended where primates with souls began. And if they don’t acknowledge that bias openly, they like to call such research a form of reductionism.
But nothing has really been reduced in this process except perhaps the dimensions of the structures under examination. The mechanistic structures may differ, but their functions are remarkably similar up and down the tree (although it seems it’s more of a bush than a tree at the moment).
if you are really interested in the subject, read the book first, then write to the author.
Artie, it’s OK, you can let it go. I forgive you.
“Oh how from the darkness of scorn we seek out the faintest gleam of pity.”
Hey Artie. Just remember when your body “chooses” to have cancer, you’ll only have yourself to blame.
What about making choices to put off making the choice of what to do about it depending on whether or not the cancer comes from a choice making virus that chose to search for a body to infect? What about choosing the right doctor, or choosing not to use alternative medicine or one of HHCs chiropractic biophysicists?
Sorry, sonic, no more pity for you.
No worries.
artfulD-
Two questions-
1) Have you read “Quantum Evolution” by Johnjoe Mcfadden?
2) Can you define ‘choice’ please? (Perhaps an example of something that has no choice would be helpful)
Haven’t read it, probably won’t, but you never know. Reviews would indicate it’s supportive of my views on the viability of some forms of self-directed evolution. Also supportive of the possibilities offered by theories such as that of the Baldwin effect.
Choice as it apples to a life form would include the ability to metaphorically ask its own questions based on sensory input and select from available options accordingly, even if it may have had at one time as little as two options. Programmed reactions to stimuli in a life form would sometimes appear to be strictly reactive, but research indicates there is virtually always some computational function involved which can override the usual automatic response.
In what we might agree are non-life forms, and where we find chemical reactions for example, some would say these involve choices and some would not, but whatever choice was involved, it would have been made outside of the control of the reactive substances – in the sense that in theory, consequences of all such reactive “choices” are consistently predictable.
Do quantum mechanics involve any choice making functions or activities? Yes, to the extent that quantum mechanics has recognized a strategic element in the operation of natural laws.
All of nature in one sense or another has made choices for itself from whatever beginning there was in its time. They weren’t, as far as we have any reason to believe, of a nature that predetermined life’s existence, or determined the nature or progress of its evolution.
And those who argue that the choices we as life forms make WERE in fact predetermined by some “quantum” or other mechanism forget, or perhaps never knew, that predetermined or not, the organisms still were and are required by circumstance to go through those particular motions.
If you disagree, be my guest. I’m no longer going to try to convince you otherwise. And I’m certainly not going to go back over any of this.
artfulD-
I don’t have a disagreement you on these issues.
From Quantum Evolution-”Life is a system that uses internal quantum measurement to capture low-entropy states that sustain the state of the system against thermodynamic decay.”
I think this is a difference between life and non-life– the choice to sustain against decay. (I think this is in line with what you are talking about)
Cheers
Well I’d argue that’s part of the dynamic that allows the system to work, but that the choices made by life forms would be for a more immediate and limited purpose. The organism’s need for energy is short term – that its choices have a long term stabilizing effect on the system would likely never be a consideration of its feedback mechanism.