As all school children know, many warm-blooded animals slip into an sleep-like state to pass part of the winter season. There is little food and the temperatures are cold, so a long nap seems like a great idea. Amazingly many of the animal’s processes shut down, including the immune system. Could this make the animal vulnerable to infection during its hibernation? And could this be the reason why animals sometimes wake up for brief periods?Recent research suggests that hibernating animals have solved the tradeoff between activating the immune system to ward off infection and conserving energy to survive the winter. As one of the researchers explained:
Our model, which is confirmed by field data, shows that torpor patterns generally seen in some hibernating animals may be an evolutionary adaptation to help protect them from bacteria that grow well in low temperatures.
So, long ago some mutations happened to create a hibernation behavior, and it worked. That is no big deal when you consider that mutations created the animal in the first place. Then some later mutations fine-tuned the behavior. This included the waking up to solve the tradeoff between fighting infections and surviving the winter. Again, not a big deal as mutations are constantly trying out new designs anyway. Once again the evidence confirms evolution.
Here's a hint - sarcasm only works when you know what you're talking about. Otherwise you just end up looking clueless and bitter.
ReplyDeleteInteresting choice to get all indignant about. The pathways of hibernation (dauer formation) in nematodes have been quite well investigated at the molecular level.
ReplyDeleteGuess what? Their pathways have considerable conservation-and some key differences-with mammals.
Here's a free review, if anyone is interested in a deeper understanding than Dr. Hunter's personal incredulity affords. And yet another example of how understanding deep evolutionary relationships impacts our understanding of disease states.
An overview of stress response and hypometabolic strategies in Caenorhabditis elegans: conserved and contrasting signals with the mammalian system.
http://www.ncbi.nlm.nih.gov/pubmed/20087441
"Studies of the molecular mechanisms that are involved in stress responses (environmental or physiological) have long been used to make links to disease states in humans. The nematode model organism, Caenorhabditis elegans, undergoes a state of hypometabolism called the 'dauer' stage. This period of developmental arrest is characterized by a significant reduction in metabolic rate, triggered by ambient temperature increase and restricted oxygen/ nutrients. C. elegans employs a number of signal transduction cascades in order to adapt to these unfavourable conditions and survive for long times with severely reduced energy production. The suppression of cellular metabolism, providing energetic homeostasis, is critical to the survival of nematodes through the dauer period. This transition displays molecular mechanisms that are fundamental to control of hypometabolism across the animal kingdom. In general, mammalian systems are highly inelastic to environmental stresses (such as extreme temperatures and low oxygen), however, there is a great deal of conservation between the signal transduction pathways of nematodes and mammals. Along with conserving many of the protein targets in the stress response, many of the critical regulatory mechanisms are maintained, and often differ only in their level of expression. Hence, the C. elegans model outlines a framework of critical molecular mechanisms that may be employed in the future as therapeutic targets for addressing disease states."
And what does the magic of hibernation largely involve? Differential gene expression and post-transcriptional regulation.
"Shotgun proteomics analysis of hibernating arctic ground squirrels."
http://www.ncbi.nlm.nih.gov/pubmed/19955082
"Mammalian hibernation involves complex mechanisms of metabolic reprogramming and tissue protection. ... Consistent with changes at the mRNA level shown in a previous study on the same tissue samples, proteins involved in glycolysis and fatty acid synthesis were significantly underexpressed at the protein level in both late torpid and early aroused animals compared with non-hibernating animals, whereas proteins involved in fatty acid catabolism were significantly overexpressed. ... Proteins involved in protein translation and degradation, mRNA processing, and oxidative phosphorylation were significantly overexpressed in early aroused animals compared with late torpid animals, whereas no significant changes at the mRNA levels between these stages had been observed. Our results suggest that there is substantial post-transcriptional regulation of proteins during torpor-arousal cycles of hibernation."
I mean, if you don't believe that regulation of metabolism, homeostasis, etc. evolved than nothing did. Just say it is all created, and get it over with. Why this system?
How did you detect design in it? By what criteria?
Cornelius -
ReplyDeleteOnce again the evidence confirms evolution.
I only know you are being sarcastic because I am familiar with you and your blog.
When you are being sarcastic about something you are supposed to make the point of view you disagree with sound ridiculous. This is something you are missing. If I didn't know you, I could quite sensibly assume you were being utterly sincere when you wrote this line.
The evidence really does confirm evolution. What's your point?
Thanks, RobertC,
ReplyDeleteThat was beautiful.
Any IDers out there care to offer the ID explanation for this observed hibernation/torpor patterns phenomenon?
ReplyDeleteAnyone?
Rob:
ReplyDelete"Interesting choice to get all indignant about."
More evidence of your inability to understand plain English.
"Here's a free review, ..."
So you're saying "evolution did it". There's nothing in the article that says how these complex mechanisms arose and no mention of evolution except in the foot notes.
How impressive.
"...This transition displays molecular mechanisms that are fundamental to control of hypometabolism across the animal kingdom. "
"...complex mechanisms of metabolic reprogramming and tissue protection. ... "
So how did the complex mechanism arise? This is where you fail ALL THE TIME - explaining how a mechanism works does not tell you where it came from!
"I mean, if you don't believe that regulation of metabolism, homeostasis, etc. evolved than nothing did"
Indeed. Your hyper exaggerations are feckless.
"How did you detect design in it? By what criteria?"
In a word, information.
Prescribed information does not and cannot arise by random unguided processes.
Algorithms with goals are contradictory to evolution at all levels.
Error detection mechanisms require pre-knowledge of correct system state.
meta-information cannot exist without intelligence.
You don't like that? Obviously!
Then leave the subject to others more intelligent than yourself.
It appears that no matter how times this is explained to you your mind is still on hold and thus why should anyone even try ... again?
Sad that none of you blind Darwhiners ever get the most basic problems with your inane theory.
Gary: "Prescribed information does not and cannot arise by random unguided processes."
ReplyDeleteThat would be the information you can't define and can't tell us how to measure.
"So how did the complex mechanism arise? This is where you fail ALL THE TIME - explaining how a mechanism works does not tell you where it came from!"
This particular paper doesn't cover that topic, just like new papers on aircraft wing design don't bother to explain Bernoulli's principle. Things that have already been conclusively demonstrated like evolutionary mechanisms don't need to be repeated, except maybe for ignoramuses like you.
"It appears that no matter how times this is explained to you your mind is still on hold and thus why should anyone even try ... again?
You mean no matter how many times you bleat your pathetic misunderstandings, no one listens anymore. But we understand.
BTW, you forgot to offer the ID explanation for this observed hibernation/torpor patterns phenomenon. Don't you have one?
Funny how evolutionists forget the onus of proof is on THEM. Intelligent design has no need for scientific proof to be declared true. Keep in mind the following things:
ReplyDelete1) Throughout history the vast sum of people have believed in a God, a greater spirit or some other ultimate entity. Non-believers have ALWAYS been the small minority. This point does not make it true but it is telling. Even today many scientists still believe in some greater power.
2) You say that life has the “appearance of design”. Considering that everything else, in human experience, where we have design that exists and serves a purpose is automatically assumed to be the production of a designer. The ONLY exception to this is evolution, and this with specified complexity found NOWHERE else in our realm of experience. The complexity and remarkable abilities of the human brain alone prove this to be true. If we were to find, in outer space, a cube shaped object 1 kilometer high, wide and deep, perfectly smooth of an unknown substance, would we assume it was just a lucky rock? No. We would assume some other civilization designed it, probably an advanced one. But life? Just happened. Aren’t we lucky.
Since everything else that has the APPEARANCE of design is actually designed except, according to you life, then the entire burden of proof is on you.
Fil: "Intelligent design has no need for scientific proof to be declared true."
ReplyDeleteThanks Fil. That's the best, most succinct argument for keeping ID in theology classes and out of science classrooms to date.
Lmao Your welcome. Scientists have been doing such a good job making the world a better place so far. I shudder to see what things will be like in 50 years. Also, I agree ID should not be taught in school. Religion should be left out of school. So should evolution. Not the science, but the incorrect assumptions you make in tying the science to evolution.
ReplyDeleteRob:
ReplyDelete"Interesting choice to get all indignant about."
Gary: "More evidence of your inability to understand plain English."
Rob: ?
Rob: ""Here's a free review, ..."
Gary: "So you're saying "evolution did it". There's nothing in the article that says how these complex mechanisms arose and no mention of evolution except in the foot notes.
How impressive."
Rob: The article did exactly what I said it did. That you don't recognize a paper comparing and contrasting pathways across evolutionary space isn't my fault. I didn't claim it investigated the deep origins of the pathways. No one article is going to have the details of the origins of all pathways. This paper compares pathways across all animals, making a compelling argument for their shared ancestry-and descent with modification.
The next quotes you choose form the paper partially makes the evolutionary argument:
"...This transition displays molecular mechanisms that are fundamental to control of hypometabolism across the animal kingdom. "
So , you choose to move the bar by asking for the origin of each pathway. They are ancient, and this is more difficult work, but if you want to know the deeper orgins of each pathway, do a Google search. Some will have clear yeast and bacterial precursors, some have newer origins.
For example:
Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom
http://www.biomedcentral.com/1471-2148/9/28
"Results
...The primordial pathway repertoire consisted of four Smads and four receptors, similar to those observed in the extant genome of the early diverging tablet animal (Trichoplax adhaerens). We subsequently retrace duplications in ancestral genomes on the lineage leading to humans, as well as lineage-specific duplications, such as those which gave rise to novel Smads and receptors in teleost fishes. We conclude that the diversification of the TGF-β pathway can be parsimoniously explained according to the 2R model, with additional rounds of duplications in teleost fishes. Finally, we investigate duplications followed by accelerated evolution which gave rise to an atypical TGF-β pathway in free-living bacterial feeding nematodes of the genus Rhabditis."
Secondly, you totally miss the point in the second paper, that much of what you propose is too complex to evolve boils down to ordinary transcriptional and post-transcriptional gene regulation.
Gary: "Prescribed information does not and cannot arise by random unguided processes. "
Directed evolution experiments, direct observation of gain-of-function in evolution, and genetic algorithms argue otherwise. Selection from a random pool begets function. So, either 'prescribed information' can arise in natural processes, or it is irrelevant in describing evolution.
Gary: "Algorithms with goals are contradictory to evolution at all levels."
Who says evolution is an algorithm with goals? I can't respond to this without some context.
Gary: "Error detection mechanisms require pre-knowledge of correct system state."
Biological error detection mechanisms work by detection of the shape of bulky DNA lesions, or by comparing lost information with the other strand in the DNA duplex or another chromosome, in genomes greater than 1n. They don't have 'knowledge.'
And more personal attacks. Why do you guys get so angry about this?
So, how was design detected in this system again?
Fil: "Also, I agree ID should not be taught in school. Religion should be left out of school. So should evolution. Not the science, but the incorrect assumptions you make in tying the science to evolution. "
ReplyDeleteWhat assumptions would those be, and what is your evidence they are incorrect?
The major assumption that evolution is true and for more details reread my post. The burden of proof is on evolutionists.
ReplyDeleteFil: You say that life has the “appearance of design”. Considering that everything else, in human experience, where we have design that exists and serves a purpose is automatically assumed to be the production of a designer. The ONLY exception to this is evolution, ...
ReplyDeleteActually, people have ascribed 'design' to the movement of planets, mountains, the flooding of rivers, winning the lottery, weather, etc.
Fil: ... and this with specified complexity found NOWHERE else in our realm of experience.
Specified complexity is not a well-defined metric.
I use the word design the way Dawkins did.
ReplyDelete“Biology is the study of complicated things that give the appearance of having been designed for a purpose.” {Richard Dawkins, The Blind Watchmaker, 1996, p. 1}
"Specified complexity is not a well-defined metric."
Another limitation of science. Is it at all defined?
""Specified complexity is not a well-defined metric."
ReplyDelete"Another limitation of science. Is it at all defined?"
Not in anyway that is meaningful. Maybe Dr. Hunter could calculate the specified complexity of hibernation for us.
Fil: "The major assumption that evolution is true and for more details reread my post.:
ReplyDeleteThat's not an assumption. It's been validated with 150+ years of positive, cross-corroborating, independent lines of evidence from a hundred different scientific disciplines. You can see/learn about it yourself in the science departments of thousands of colleges and universities, and in natural history museums around the world. There is also a ton of evidence readily available online.
What about the part where you show all that evidence is wrong? It's not in your previous post.
The burden of proof is on evolutionists.
That burden has been met to the satisfaction of >99% of the scientific and academic communities.
RobertC: " Maybe Dr. Hunter could calculate the specified complexity of hibernation for us."
ReplyDeleteI'd be happy if any IDer anywhere could show an actual 'specified complexity' calculation for any biological object. But I'm not holding my breath.
Fil: I use the word design the way Dawkins did. “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” {Richard Dawkins, The Blind Watchmaker, 1996, p. 1}
ReplyDeleteYes, and people have ascribed all those traits to the movement of planets, the weather, etc. Looking designed to you is not sufficient to reach a scientific conclusion. That requires the proposal and testing of hypotheses.
Gary states: "Prescribed information does not and cannot arise by random unguided processes.
ReplyDeleteFirstly, I wonder what you mean by prescribed? DNA is not prescribed information. It lacks specification, as evidenced by the great variation amongst homologous genes - cytochrome b, for example. Amongst sequences for cyt b for a couple hundred small mammals, there is as little as 25% sequence identity across this taxomically restricted phylogeny - in a crucial, highly expressed gene, no less. The idea that DNA sequences are somehow prescribed is is a fundamental misunderstanding or misrepresentation presented by the ID movement.
Secondly, no one talks about random unguided processes generating functionality. In evolutionary theory, the the stochastic process of mutation is not teleologically guided, but it is teleonomically guided by natural selection towards higher phenotypic fitness - of which a substantial factor is gene functionality.
I'm a little confused. Did the animals evovle hibernation first? But then they would die from infections. Did they evolve the pattern of waking up from hibernation first? But how can you wake up from hibernation if you don't yet hibernate?
ReplyDeleteNat -
ReplyDeleteNot every hiberbating animal dies of infection if they don't wake up. They just run a greater risk of it.
Presumably hibernation carries less risk than trying to survive the winter fully conscious. So hibernation increases survival chances. Then interupted hibernation is yet another improvement since it keep the immune system active.
"In evolutionary theory, the the stochastic process of mutation is not teleologically guided, but it is teleonomically guided by natural selection towards higher phenotypic fitness - of which a substantial factor is gene functionality."
ReplyDeleteabimer could you explain the differences between teleologically and teleonomically?
what do you mean by higher phenotypic fitness'
"I'm a little confused. Did the animals evovle hibernation first? But then they would die from infections. Did they evolve the pattern of waking up from hibernation first? But how can you wake up from hibernation if you don't yet hibernate?"
ReplyDeletenatschuster,
Speaking as one brother to another (I presume), please try to understand your opponent's arguments before you mock them. When you don't it just makes you look foolish. It is clear from your comment that you are not familiar with how natural selection works. Hibernation evolved first, of course. But even without a mechanism like the one mentioned in the article to ward off infection, hibernation would still be beneficial, because it conserves energy in the lean months. Not every animal that hibernated would get a bacterial infection. Not every animal that got a bacterial infection would die from it. The ones who did get an infection would have to divert resources (calories, nutrients) to fighting off the infection that could otherwise have been used for reproduction. So if an adaptation arose that enabled an animal to fight off infection better than its competitors, that trait would statistically spread through the population faster.
Blas asks: "abimer could you explain the differences between teleologically and teleonomically?
ReplyDeletewhat do you mean by higher phenotypic fitness' "
Teleology is goal-seeking activity, teleonomy is goal-directed activity. While the distinction may seem subtle, it is important. The former requires awareness of the goal, the latter does not. Gravity is teleonomic in this sense - drop a rock off a cliff and it will fall. It is directed to the ground, but of course it is not 'trying' to reach the ground. By contrast, a person getting in a car and driving to work is an example of a teleologic activity.
The action of natural selection is teleonomic. It is blind to any long-term goals, but it nonetheless acts like a force in the short-term on phenotypic fitness.
This leads into your second question: classically defined, phenotypic fitness is a measurement of the ability of a phenotype (i.e. the product of a genotype - e.g. a bacterium, a human, a seaweed) to reproduce. This is meaningful in the context of natural selection only when such fitnesses are considered relative to the fitnesses of other phenotypes. The one better equipped to reproduce will, on average, leave more viable offspring.
So, selection acting on the size or shape of the beaks of seed-eating finches is simply the response to the size of available seed - the phenotype's ability to exploit the resource, rather than a force deliberately shaping the beak.
abimer,
ReplyDeleteYou have one problem with claiming natural selection to be teleonomic in the same sense as a rock under influence of gravity. It is the fact that you presuppose the "force" of natural selection to be "natural" in the same sense as gravity. I will give it more serious thought when you can show me a single equation for "natural selection" acting on organisms that is as elegant and accurate as Newtonian or Einsteinian physics for that matter.
There is no physical relationship between an organism and the objective to survive. Claiming that it just "want" to replicate because it can is begging the question... again. That alone requires Teleology.
Michael: I will give it more serious thought when you can show me a single equation for "natural selection" acting on organisms that is as elegant and accurate as Newtonian or Einsteinian physics for that matter.
ReplyDeleteBiology is rarely as simple as physics, but here are a few important relationships: Fisher's Fundamental Theorem of Natural Selection, Hardy–Weinberg Equilibrium, Price Equation, as well as various simple relationships concerning rates of fixation with or without natural selection. There's an entire scientific field, population genetics, which studies these relationships. A couple of simple examples:
The probability of fixation of a beneficial mutation in a large population is 2s, where s is the selection coefficient << 1.
The rate of fixation of neutral mutations is equal to the neutral mutation rate.
Did the animals evovle hibernation first? But then they would die from infections.
ReplyDeleteNot at all, one can imagine that some did not die. And if it is observed that some animals of a similar species do not hibernate then one could imagine that all those that did went extinct. In fact, if it was observed that no animals at all hibernated then "theories" of natural selection would explain that equally well. And if it was observed that some animals did not sleep at all, again explained. Or if they got up and did a little dance at midnight each night, that would be explained perfectly. After all, they're alive so they're obviously the fittest and therefore survived.
E.g.
Not every hiberbating animal dies of infection if they don't wake up. They just run a greater risk of it.
Presumably hibernation carries less risk than trying to survive the winter fully conscious. So hibernation increases survival chances.
After all, whatever is alive now has survived so it must be the fittest, except when it dies and is not. In any event, clearly "theories" of natural selection explain all life because it is, after all, alive or fit.
Thanks, RobertC,
ReplyDeleteThat was beautiful.
Lol! This reminds me of Chesterton's comment on Darwinian charlatanism of another sort:
Most Eugenists are Euphemists. I mean merely that short words startle them, while long words soothe them. And they are utterly incapable of translating the one into the other, however obviously they mean the same thing. Say to them “The persuasive and even coercive powers of the citizen should enable him to make sure that the burden of longevity in the previous generation does not become disproportionate and intolerable, especially to the females”; say this to them and they will sway slightly to and fro like babies sent to sleep in cradles. Say to them “Murder your mother,” and they sit up quite suddenly. Yet the two sentences, in cold logic, are exactly the same.
(Eugenics and Other Evils: An Argument
Against the Scientifically Organized Society
by G.K. Chesterton)
There is little evidence that the origins of hibernation is explained in terms of random mutation and natural selection. One of the main problems with such a view is that it is reasonable to assume organisms are, in fact, alive. Much like we are, which is what another commenter rather reasonably assumes here:
Teleology is goal-seeking activity, teleonomy is goal-directed activity. While the distinction may seem subtle, it is important. The former requires awareness of the goal, the latter does not. Gravity is teleonomic in this sense - drop a rock off a cliff and it will fall. It is directed to the ground, but of course it is not 'trying' to reach the ground. By contrast, a person getting in a car and driving to work is an example of a teleologic activity.
Actually some people would disagree with that. After all, that person is probably going to work to provide for their family (just as theories of natural selection would predict) and that can be explained purely in terms of blind and ignorant processes.
But yes, let's be reasonable and admit that we are sentient beings who see and feel and that we are aware of the future, have goals, knowledge, etc. So why assume that other organisms are never aware of such things? Why try to imagine things about the past in order to show that the awareness typical to organisms never has an impact on anything? In any case, imagining things about the past is a form of unfalsifiable pseudo-science which can be rejected on those grounds alone. Mechanistic philosophy is abysmally ignorant and unfathomably stupid given what we already know so one shouldn't be surprised that it also leads to pseudo-science.
Biology is rarely as simple as physics, but here are a few important relationships...
ReplyDeleteNone of which predict that there are trajectories of adaptation based solely on random mutations leading to the origins of things like sleep or hibernation. But look at what another commenter already said: Gravity is teleonomic in this sense - drop a rock off a cliff and it will fall. It is directed to the ground, but of course it is not 'trying' to reach the ground. By contrast, a person getting in a car and driving to work is an example of a teleologic activity.
But if that's the case in the case of people then why not other organisms? And why have those who presumably mean to establish a "scientific" theory that is the epistemic equivalent of the theory of gravity always used words which imply teleological activity beginning with natural "selection" and "struggle." After all, nothing is selecting and nothing is struggling because everything in biology can be reduced to blind and ignorant processes according to those ignorant and stupid enough to try to support such a view. Maybe that's the problem, once they've reduced themselves to ignorant processes they become imbeciles who can't say what they mean due to a lack of integrity. Perhaps that's why asking Darwinists to specify a scientific theory in the language of mathematics/integers which can be verified or falsified based on empirical evidence is the material of satire. They're usually too busy imagining things about the past or playing pretend that population genetics supports Darwinian creation myths.
mynym: There is little evidence that the origins of hibernation is explained in terms of random mutation and natural selection.
ReplyDeleteWe have to start by establishing Common Descent, then having established the general history of evolutionary divergence, then we can study the various mechanisms involved.
Zachriel: Biology is rarely as simple as physics, but here are a few important relationships...
mynym: None of which predict that there are trajectories of adaptation based solely on random mutations leading to the origins of things like sleep or hibernation.
That wasn't the question raised.
We have to start by establishing Common Descent...
ReplyDeleteYou start by assuming common descent because there can never be evidence of common design of any sort according to your philosophy. Even if all organisms shared a similar type of sentience to one degree or another that shaped their commonality you would still be blind to it and imagine that it was evidence of common descent. This is as it must be no matter what is observed because the impact of sentience, knowledge and teleology on reality is the equivalent of "magic" to Darwinists.
Common descent is assumed as it must be given the rise of mechanistic philosophy in modern times, not established.
mynym: You start by assuming common descent because there can never be evidence of common design of any sort according to your philosophy.
ReplyDeleteOf course there can, there's just no scientific evidence to support the contention.
mynym:
ReplyDelete"You start by assuming common descent because there can never be evidence of common design of any sort according to your philosophy."
The accusation that acceptance of common descent is based solely on philosophical motives is a recurring theme in these threads.
I can't speak for others, but I am a conservative Christian and I fully accept common ancestry. I was a young earth creationist for most of my life, and at first, acknowledging that the evidence is overwhelmingly in favor of evolution, (especially the molecular data) was terribly difficult.
I have always been very interested in science, and probably would have pursued paleontology had not my creationist upbringing corrupted my perception of science. (as it seems to have done to many people here)
Since my theology (or philosophy as you might say) was married to the idea of a young earth and special creation, no amount of evidence could have changed my mind. Even when presented with molecular evidence that now seems irrefutable, In my mind I could justify ignoring it by claiming that God must have designed things that way for some reason. Perhaps He wanted to just make it look like things evolved, to test our faith. Or perhaps Satan had somehow figured out how to tinker with DNA in order to fool us. Anything but common ancestry.
It wasn't until I realized the error in my theology that I was able to step back and evaluate all the evidence fairly, without the deep confirmation bias that had previously afflicted me. For me, it was realizing that if my faith was in alignment with the truth, then *anything* that was true was compatible with it, including evolution
The idea that people only accept common ancestry because of their philosophical disposition is nonsense. I accepted evolution *despite* my philosophical/theological disposition, and I must say that I consider my theological worldview more informed and consistent, not less.
No matter what patterns you find in nature, you can always say "Well, God must have designed it that way." But if those patterns are exactly what one would have expected common ancestry to produce, You must ask yourself why that is the case. (and when I say 'what one would have expected,' I mean what real scientist would have expected, not the straw men Cornelius likes to imagine)
So the idea that everyone who accepts evolution for philosophical reasons and not because the evidence, fairly evaluated, overwhelmingly indicates such, is pure baloney. (I'm sure some people accept it for philosophical reasons; but I'm sure many more people accept creationism for philosophical reasons alone.)
Derick:
ReplyDelete===
No matter what patterns you find in nature, you can always say "Well, God must have designed it that way." But if those patterns are exactly what one would have expected common ancestry to produce, You must ask yourself why that is the case. (and when I say 'what one would have expected,' I mean what real scientist would have expected, not the straw men Cornelius likes to imagine)
===
What straw men are referring to?
Derick:
ReplyDelete===
the evidence is overwhelmingly in favor of evolution, (especially the molecular data)
===
Can you give an example?
Michael says: "You have one problem with claiming natural selection to be teleonomic in the same sense as a rock under influence of gravity. It is the fact that you presuppose the "force" of natural selection to be "natural" in the same sense as gravity. I will give it more serious thought when you can show me a single equation for "natural selection" acting on organisms that is as elegant and accurate as Newtonian or Einsteinian physics for that matter."
ReplyDeleteThere is a body of mathematics on natural selection in contemporary population genetics. There is also a body of work around stochastic fixation of neutral and nearly neutral alleles in the literature. If you want some an equation re selection, I guess the most basic one is that the probability of fixation of a mutation under selection is 2s/(1 - e^(-4Ns)), where s is the selection coefficient and N is the population size.
I originally put quote marks around force precisely because natural selection is not a force like gravity. It is a filter. The patterns produced in a population experiencing mutation in each individual in each generation will never produce the pattern of an elegant Newtonian force nor would we expect it to. Selection is a filter reflecting the influence of heritable differences on the survival and reproduction of taxa, but let's be clear it is not a sole determinant of survival or reproduction - much of this is stochastic.
abimer,
ReplyDeleteWill you be able to create your own critical evaluation about your claim that natural selection is a force established like gravity?
Above you make a lot of clanging noises because the math you talk about are exactly the type of math that is also used to evaluate and predict the actions of intelligent agent i.e. human populations.
What you are actually getting at is a potential candidate for explaining the difference between the act of nature vs. the act of intelligence.
Let my make a broad stroke attempt:
Natural phenomenon act according to fundamental physics but intelligent agents act by altering natural patterns and the effect can be measured by information theoretic calculations.
or
Natural patterns only arise according to the rules of nature vs. intelligent agents alter natural patterns contrary to natural laws.
With this said:
abimer, please show me the natural phenomenon that creates DNA message patterns.
P.S.
ReplyDeleteMy attempt to a definition was informed by Hubert Yockey's definition of living organisms:
"The existence of a genome and the genetic code divides living organisms from nonliving matter. There is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences."
http://www.amazon.com/Information-Theory-Evolution-Origin-Life/dp/0521802938/ref=sr_1_1?ie=UTF8&s=books&qid=1275039548&sr=8-1
Michael says: "What you are actually getting at is a potential candidate for explaining the difference between the act of nature vs. the act of intelligence."
ReplyDeleteWell, perhaps. But if human intelligence is considered a part of nature - an emergent property of our biochemical complexity - there is no clear distinction here. Animals can also disturb what you seem to be referring to as natural patterns e.g. beavers building dams, birds building nests etc.
"abimer, please show me the natural phenomenon that creates DNA message patterns."
The natural phenomenon at base is mutation - which is a probabilistic chemical reaction. The most basic form of mutation, which suffices for the discussion here, is the point mutation - the single substitution of one nucleotide for another.
The mechanisms of mutation are well understood and documented, involving, for example, tautomerization or deamination (via hydrolysis). Point mutations are often biased chemical reactions. When CG dinucleotides occur, the C is often methylated. This makes it prone to deamination, where it is replaced by T. Numerous cellular compounds including reactive oxygen species created during metabolism are also responsible for DNA damage which can result in mutation.
In mitochondrial DNA, the effects of biased mutation via known mechanisms are obvious in biased base composition. mtDNA is interesting - it features asymmetric replication where one strand is always exposed for longer periods than the other. Because of mutation bias, this causes an accumulation of T and G on the heavy strand and of A and C on the light strand.
Most interestingly, because we know the frequency of these mutations and because there is neither an empirical nor a theoretical basis to suggest mutations are more likely at any of the three sites in a codon - after they are simply strung together in a chain and can be read from different reading frames - we can directly observe the effects of purifying selection upon base composition in species.
It is a ubiquitous pattern in metazoan mtDNA that the the base composition bias is strongest at the third codon position, while composition is most equal at the second position and in between at the first position. Why should this be? Well, mutations at the third codon position are far less likely to change the amino acid produced. And first position changes are far more likely to produce chemically similar amino acids. Hence, the base composition bias in mtDNA clearly and unambiguously reflects the actions of natural selection.
Thus we can observe the natural phenomenon of known chemical reactions altering nucleotides in a DNA sequence and the natural selection acting with various strength on the population level to mutation.
P.S. Michael, I realise that you absolutely won't accept that mutation, filtered by selection, could conceivably result in functional DNA and that my entire response will be wholly unsatisfactory to you.
ReplyDeleteThe only I think I would ask that you bear in mind for any response is what I have already pointed out in this thread earlier - that genes do not necessarily have high levels of ordered specification that one might expect from an intelligent code. The patterns of mutation are all over them.
abimer,
ReplyDeleteI am interested in having an explanation for the relationship between:
* "The observed mechanism of "natural phenomenon of known chemical reactions altering nucleotides"
vs.
The observed mechanism that is repairing the genetic code, by using genetic code based mechanisms.
vs.
The observed mechanism of genetic code that actively dictate/instruct the outcome of the chemical reaction.
vs.
A chemical reaction that mutate the code.
Can you critically review these relationships in relation to the above explanation you proposed?
There is very clear evidence that code based machines are exposed to signal degradation, due to natural causes & intelligent causes, but you have far to go to be convincing that degradation ultimately leads to new novel information. Evidence for the contrary is ample and agree with observations of other code based systems. For example:
* We all know the effects of a gene pool that becomes too "shallow". Is this problem not caused by the amplification of errors that leads to predominantly undesirable modifications in the organism?
* We know what corrupts PC hard drives
* Was the e-coli benefits reported not at the cost of losing some other ability or simply caused by selective breeding that accentuated existing traits?
All in all. These phenomenon where code based mechanisms are at play (nature PLUS information)is vastly more different than gravity and the difference can be observed... It is CODES.
P.S. I never excluded animals or any biological feature from causing non-natural patterns. I see all life as coding machines, some autonomous and others not.
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ReplyDeleteI forgot to ask:
ReplyDeleteIs there not a known ratio between beneficial mutations vs. (uncorrected) non-beneficial mutations? What is that ration and what is the significance for the proposed mechanism of evolution?
Michael: I will give it more serious thought when you can show me a single equation for "natural selection" acting on organisms that is as elegant and accurate as Newtonian or Einsteinian physics for that matter.
ReplyDeleteYou never acknowledged the answers you were provided to your comment.
Has any evolutionist or group ever done a probabilistic study, taking into account all know "mutations" into every "species" that we are certain to have existed in the time known to have been available on earth? ie. we started with such and such organism and it mutated into this taking this long, etc. until the entire available tree is mapped out. That would be interesting to see....
ReplyDeleteMichael says:"Is there not a known ratio between beneficial mutations vs. (uncorrected) non-beneficial mutations? What is that ration and what is the significance for the proposed mechanism of evolution? "
ReplyDeleteNo there is not a single ratio, although estimates have been made in some model organisms, such as Drosophila. The single ratio idea itself indicates a misunderstanding of molecular evolutionary processes. A rudimentary aspect of integrating ecology with molecular population genetics is that the proportion of beneficial mutations will depend on the fit to the environment, and the scope for beneficial mutations to occur.
See: http://210.193.216.98/cps/rde/papp/techAdvice:techAdvice/http://www.pnas.org/content/106/32/13415.full
and
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060060
for simple demonstrations of both points respectively in garter snakes.
Further beneficial mutations are no less likely to be corrected than non-beneficial ones, as you imply here (in fact, mutation refers to uncorrected DNA damage). It is also necessary to further break down non-beneficial mutations into effectively neutral mutations and deleterious mutations. It should be clear that mutations do not necessarily universally belong in one category, as the mutation illustrated in the first garter snake article above demonstrates.
The significance is that although the process is complex, we can frequently observe phenomena for which the only explanation is the interaction between ecology and genetics via natural selection.
Michael says:"There is very clear evidence that code based machines are exposed to signal degradation, due to natural causes & intelligent causes, but you have far to go to be convincing that degradation ultimately leads to new novel information. Evidence for the contrary is ample and agree with observations of other code based systems. For example:
ReplyDelete* We all know the effects of a gene pool that becomes too "shallow". Is this problem not caused by the amplification of errors that leads to predominantly undesirable modifications in the organism?"
Indeed, but that is half a story. The point from the evolutionary perspective is that the imbalance between deleterious and beneficial mutations can be overcome by sufficient population size, via population genetic mechanisms based on selection. You refer to inbreeding, which is the effect of increasing homozygosity on slightly deleterious traits in non-haploid organisms. Increased genetic diversity from larger population sizes overcomes this problem - the other side of the coin that you are forgetting about.
"* We know what corrupts PC hard drives"
This is a terrible analogy that I will not discuss in any depth. Computer data and DNA are not similar, nor are the processes that degrade them, nor are the effect of changes to them, nor does any population-level evolutionary process have any analogy in computing.
"* Was the e-coli benefits reported not at the cost of losing some other ability or simply caused by selective breeding that accentuated existing traits?"
You refer, I assume, to changes in citrate metabolism in E. coli from Richard Lenski's lab in a now 50,000 generation experiment.
It is not a selective breeding programme, although the lab conditions are undoubtedly idealised. Existing traits were not simply accentuated, the strain developed the ability to metabolise a new energy source. A non-laboratory example has of course been observed in nylon-degrading bacteria. Is it not amazing that in the course of only decades, substantial changes to metabolic pathways can be observed?
I cannot make you believe that the population-level processes of selection is what filters the genetic treasure from the trash sufficiently to not only sustain life but have it increase in complexity over billions of years. You will have to suspend your own disbelief if you wish to openly investigate the possibility.
However, for the third time, it is the lack of specificity in gene sequences, along with the signature of primarily neutral genetic change, and the population processes that enable this change to be sustained are points that defy an interpretation of intelligent intervention for the origin and maintenance of genetics and genomes.
Derick: the evidence is overwhelmingly in favor of evolution, (especially the molecular data)
ReplyDeleteCornelius: Can you give an example?
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The existence of and patterns of pseudogenes, (especially the GULO gene in humans & apes and the the mutated remains of the vitellogenin gene); High synteny in closely related species; and the pattern of cytochrome C mutations in different species, are just a few that come to mind.
The problem with ID as a scientific proposition is that, unlike common ancestry, it could conceivably explain anything: "Well, the designer could have made it that way for a for some odd reason. the IDer works in mysterious ways." That does not make it a better 'explanation.'
I'll be the first to admit that theology is much simpler {not necessarily better, but simpler} if God just created everything directly and Genesis is a literal account of history. And a small part of me would just love for evolution to be falsified in some way so I could go back to having an unambiguous physical 'proof' of God. But when I step back and look at the evidence from an unbiased standpoint (or as unbiased as I possibly can,) common ancestry is by far the best explanation of the what we see in nature. If God didn't ordain some process of evolution involving common ancestry to create us, He sure went well out of His way to make it look like He did.
As for your 'scientific straw men'; I don't think anything could illustrate it better than your article on whale evolution on June 1st. You paint the picture of a scientific community befuddled by the fact that the ancestors of whales evolved at an irregular pace. As Zachriel pointed out, even Darwin predicted this:
"...it is probable that the periods, during which each {species} underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition."
Incredibly, you have taken a fulfilled prediction of evolution, and classified it as a falsified prediction. Frankly, it's embarrassing to watch a fellow Christian spew such distorted thinking. If you're going to point out failed predictions of evolutionary theory, fine, I'm sure there are plenty; the pace of whale evolution certainly isn't one, and neither are the differences in the human and chimp y-chromosome, nor is 'complexity', or just about anything else you've written about lately.
Derick:
ReplyDelete====
The idea that people only accept common ancestry because of their philosophical disposition is nonsense. I accepted evolution *despite* my philosophical/theological disposition, and I must say that I consider my theological worldview more informed and consistent, not less.
...
the evidence is overwhelmingly in favor of evolution, (especially the molecular data)
...
The existence of and patterns of pseudogenes, (especially the GULO gene in humans & apes and the the mutated remains of the vitellogenin gene); ...
====
So you say your theology plays no role, and yet you cite metaphysically-laden arguments such as pseudogenes. From a scientific perspective you have a successful prediction--hardly overwhelming evidence. But from a theological perspective, it becomes overwhelming because it falsifies design/creation:
http://darwins-god.blogspot.com/2009/06/evolutions-religion-revealed.html
These theological arguments have been used over and over for centuries. Of course your theology is at play here.
Derick:
ReplyDelete===
The problem with ID as a scientific proposition is that, unlike common ancestry, it could conceivably explain anything: "Well, the designer could have made it that way for a for some odd reason. the IDer works in mysterious ways." That does not make it a better 'explanation.'
===
Yet more metaphysics. You seem to be so deep in that you're unaware of it.
Derick:
ReplyDelete====
As for your 'scientific straw men'; I don't think anything could illustrate it better than your article on whale evolution on June 1st. You paint the picture of a scientific community befuddled by the fact that the ancestors of whales evolved at an irregular pace. As Zachriel pointed out, even Darwin predicted this:
"...it is probable that the periods, during which each {species} underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition."
Incredibly, you have taken a fulfilled prediction of evolution, and classified it as a falsified prediction. Frankly, it's embarrassing to watch a fellow Christian spew such distorted thinking. If you're going to point out failed predictions of evolutionary theory, fine, I'm sure there are plenty; the pace of whale evolution certainly isn't one, and neither are the differences in the human and chimp y-chromosome, nor is 'complexity', or just about anything else you've written about lately.
====
This illustrates the degree to which evolution is protected. Complexity for which evolution has no explanation? No problem. Substantial differences between the human and chimp y-chromosome which were unexpected? No problem. How wrong to think they are anything but fulfilled predictions.
CH:No problem. How wrong to think they are anything but fulfilled predictions."
ReplyDelete------------------------------
I never insinuated they were 'fulfilled' predictions or anything of the sort.
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CH: "Substantial differences between the human and chimp y-chromosome which were unexpected? "
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An evolutionary NON-prediction is not the same as an evolutionary FAILED prediction; But I don't know what book on evolution you're reading if you think that evolution doesn't predict differences in the DNA of different species.
I'm halfway expecting one of your future articles to elaborate on how the current stock market value is yet another failed prediction of evolution.
CH: "So you say your theology plays no role, and yet you cite metaphysically-laden arguments such as pseudogenes"
ReplyDeleteI apologize Cornelius, for a moment I mistook Intelligent Design for a scientific proposition; I forgot that any argument against it is 'metaphysical' by default.
Cornelius, you seem to be a very intelligent man. But you continuously make the error of thinking that anything that has a metaphysical *implication* is necessarily a metaphysical question, or is arrived at by metaphysical reasoning. That is not the case at all.
For example, the statement: "Jesus Christ rose from the grave on the third day after his death on the cross," Is a 100% empirical question; that is, it, in principle, could be tested scientifically. You could conceivably find evidence that says 'Yes he did' or 'no he didn't'. A time machine would settle the question definitively. Now, the implications of that statement *are* metaphysical; but the question of *whether or not* it happened is entirely empirical.
I used to consider ID a valid scientific hypothesis; but the more I hear proponents respond "Who says God couldn't have just made it that way?" as a rebuttal to all arguments, the less I'm inclined to consider it so.
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ReplyDeleteDerick: The problem with ID as a scientific proposition is that, unlike common ancestry, it could conceivably explain anything: "Well, the designer could have made it that way for a for some odd reason. the IDer works in mysterious ways." That does not make it a better 'explanation.'
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Cornelius: "Yet more metaphysics. You seem to be so deep in that you're unaware of it."
-------------
How exactly is pointing out the fact that ID makes no falsifiable scientific predictions 'deep' in metaphysics?
Derick:
ReplyDelete====
CH: "So you say your theology plays no role, and yet you cite metaphysically-laden arguments such as pseudogenes"
I apologize Cornelius, for a moment I mistook Intelligent Design for a scientific proposition; I forgot that any argument against it is 'metaphysical' by default.
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Except that I didn't say that.