Responding to Moran – Is “Unguided” Part of Modern Evolutionary Theory?

_{Jonathan Bartlett

August 12, 2012

Intelligent Design}

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I am always aghast that in the 21st century people still make the claim that mutations are unguided. This is a hold-over idea from before the discovery of DNA, simply because some mutations were found to occur independently of selection.

However, modern evidence has showed that mutations are actually in large part due to mechanisms geared for adaptive purposes, just like the rest of biology. And, just like hearts have heart attacks, mutation systems can break down, too, and lead to disease. Just like bacteria, we discovered mutations first by noting the ones that were causing disease, but with every closer look we see that these are the exception rather than the rule.

To point to a simple example (and one that is even often used as definitive evidence of the efficacy of random mutations!) let’s look at the somatic hypermutation process in the immune system. When a new bacteria invades the body and causes an infection, the body must generate a new gene. So what does it do? It takes a close-fitting antibody gene and mutates it. Now, first of all, you should notice that the mutations only happen in the correct gene – the antibody gene. That’s 1,200 base pairs out of 3,000,000,000. But that’s not all – it also focuses mutations on the part of the gene that attaches to the antigen, not the part that signals the cell (because otherwise it wouldn’t signal the cell correctly). So, that’s roughly 600 base pairs out of 3,000,000,000. The mutation system is highly selective of the sites that it mutates, skipping over the cell signaling systems and focusing on the part that is specific to the antigen.

So, therefore, in this scenario (which is one of the best-studied), teleology (goal-directedness) accounts for 99.99998% of the specificity of the mutation, and randomness / unguidedness / happenstance accounts for 0.00002% of it. Yet somehow the myth persists that we have good evidence that mutations are random.

For more information on this issue, you might be interested in a UD series I did on the modern synthesis and the video below:

—–

P.S. I originally tried to post this comment on Moran’s blog itself, but was having technical difficulties. So, if it winds up in his moderation queue three or four times under different accounts, I’m sorry, I was just trying to get it posted.

Comments

mphillips
Mutations being directed are the provenience of ID.
Hardly. Are you certain you're using the word provenience correctly? Living organisms are themselves the source of directed mutations. Catch up on the latest science please.Mung_{August 21, 2012
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mphillips you claim that there is no evidence of deterioration and yet the fitness test conducted by Dr. Cano showed a loss in 'fitness. But when shown this evidence you state: "Seems to me the opposite",,, Perhaps you should take a closer look at exactly what 'the fitness test' measures so that your 'seems to' misconception can be corrected:
Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248
As to your quote ,,, 'filling their ecological niches quite well',,, nothing like assuming your conclusion into the very question being asked so as to insure you get the answer you want, is there mphillips??? i.e. Immunity bacteria are shown to be species specific (Regardless of the surprising result, Darwinists still insist evolution did it.)
Our Microbes, Ourselves: Billions of Bacteria Within, Essential for Immune Function, Are Ours Alone - ScienceDaily (June 21, 2012) Excerpt: Chung repeated the experiment, only this time populating a third group of mice with microbes common to rats. This new group showed the same immune system deficiency as the humanized mice. "I was very surprised to see that," Chung said. "Naturally, I would have expected more of a half-way response." http://www.sciencedaily.com/releases/2012/06/120621130643.htm
As to calculating varying rates of genetic entropy for different forms of life, which I hold large populations of bacteria to be extremely resistant to, you can use this computer program to get a ballpark figure:
Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load: Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE http://mendelsaccount.sourceforge.net
Also of note:
DNA Degeneration: Top Population Geneticists agree neo-Darwinism is not supported by the data – John Sanford http://www.youtube.com/watch?v=tYEkqwOXE5U Genetic Entropy - Dr. John Sanford - Evolution vs. Reality - video (Notes in description) http://vimeo.com/35088933
further notes:
AMBER: THE LOOKING GLASS INTO THE PAST: Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms. http://bcb705.blogspot.com/2007/03/amber-looking-glass-into-past_23.html Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330
bornagain77_{August 19, 2012
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ba77,
a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains.
Seems to me the opposite. Modern strains have a better or just different diet. Therefore they have evolved. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. In that specific example, perhaps. And so? The point is that every human is "infected" by more then 200 strains of bacteria, adults have between 11,000 (forearm) and 1.5 million (scalp) bacteria per square centimeter of skin. So if your claim was true, then nobody as told all these bacteria as they seem to be filling their ecological niches quite well indeed. If we can have many generations of bacteria how many will have to pass before we notice any sign at all of this inevitable deterioration you claim is happening?mphillips_{August 19, 2012
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mphillips falsely believes:
If we look at the fossil record we don’t see a pattern of deterioration. If we look at a bacteria over many generations we don’t see a pattern of deterioration.
Yet the truth is:
Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory – Cornelius Hunter - July 2012 Excerpt: Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time. http://darwins-god.blogspot.com/2012/07/evolutionists-are-losing-ground-badly.html The Cambrian's Many Forms Excerpt: "It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.""From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,"....(Yet Surprisingly)...."There's hardly any variation in the post-Cambrian," he said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites." University of Chicago paleontologist Mark Webster; article on the "surprising and unexplained" loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago. http://www.terradaily.com/reports/The_Cambrian_Many_Forms_999.html
In fact, the loss of morphological traits over time, for all organisms found in the fossil record, was/is so consistent that it was made into a 'scientific law':
Dollo's law and the death and resurrection of genes: Excerpt: "As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo's law, after its propounder, and is taken as a general statement that evolution is irreversible." http://www.pnas.org/content/91/25/12283.full.pdf+html A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html
as to ancient bacteria:
The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland's work: “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961
In reply to a personal e-mail from myself, Dr. Cano commented on the 'Fitness Test' on the ancient bacteria, I had asked him about:
Dr. Cano stated: "We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.": Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki
Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.bornagain77_{August 19, 2012
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The point is what you can demonstrate.
Well it is clear that you cannot demonstrate anything beyiond ignorance and belligerence.Joe_{August 19, 2012
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The mechanics behind directing every mutation rules out your position as impracticable, if for no other reason.
Nice strawman.
Are you really proposing that “the designer” reaches in and directed every single mutation?
Nope, never said nor implied such a thing.Joe_{August 19, 2012
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Joe,
Therefore it would be more relevant were you to show that they are undirected, rather then placing the onus on others who are not making that claim.
The mechanics behind directing every mutation rules out your position as impracticable, if for no other reason. We'd have noticed by now! Are you really proposing that "the designer" reaches in and directed every single mutation? That's laughable. I'd suggest you search google scholar for "spontaneous mutations" but then you'd simply reply "there's nothing there that proves the mutations are not really directed after all" or perhaps "you can't use what you are trying to explain to explain the origin of the thing you are talking about". You seem to use those two alot.mphillips_{August 19, 2012
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johnnyb,
In other words, in any reasonable population genetic scenario, you are going to primarily get de-evolution rather than evolution.
So why don't we see bacteria "de-evolving" over the many thousands of generations we are able to observe them over? Where can I see this "devolution" in action, in near-real time? If it's as ubiquitous as you claim....mphillips_{August 19, 2012
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Joe,
Mutations can be random wrt fitness and still be directed.
Of course. And many other things might be true as well. The point is what you can demonstrate. You should, however, be able to understand this: http://evolution.berkeley.edu/evosite/evo101/IIIC1bLederberg.shtml In 1952, Esther and Joshua Lederberg determined that many of the mutations for antibiotic resistance existed in the population even before the population was exposed to the antibiotic — and that exposure to the antibiotic did not cause those new resistant mutants to appear. So if mutations were indeed "directed" as you claim Joe then the results would have been different. Or perhaps this is just a special case and the designer knew it was an experiment and did not do what it usually does?mphillips_{August 19, 2012
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mphillips- Mutations being undirected are the provenience of the theory of evolution. Therefore it would be more relevant were you to show that they are undirected, rather then placing the onus on others who are not making that claim.
If you are genuinely interested on why it is generally accepted that mutations are random with respect to fitness then there is plenty of reading material out here.
LoL! They have to random, period. Mutations can be random wrt fitness and still be directed. So what do YOU have besides your belligernece towards ID?Joe_{August 19, 2012
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"Why is it that it has to be corrupted design?" It doesn't have to be corrupted design. It is funny that my every side note of options is being interpreted as a dogmatic statement. Whether or not the design is original or corrupted is not part of ID, at least at the present moment. "Perhaps you could give a few examples of designs that are still as the designer intended them to be and some which are not?" Again, I could list things that *I* think are corrupted, but that is not part of ID proper. I will refrain from listing them because you have trouble distinguishing between when I am conjecturing and presenting reasoned arguments. "But this is an argument that HIV is designed in it’s current form" It's an argument that the mechanism you mention is designed in it's current form. Also note that one form of corruption is simply being out-of-place. Of course, I shouldn't say any of this, because you will think that I'm telling you an established ID position. "Why “is it likely”? So you want to have it both ways, even if it can be shown to have evolved then it evolved that way due to programmed directions." Which two ways do I want to have it? The reason why it is likely is because (a) there is no empirical evidence that natural selection acting on random mutations alone can build the sort of structures needed, (b) there is theoretical reasons to think that it can't (see here and here), (c) there is empirical evidence to show that interesting mutations do happen as the result of prior information being present in the genome (see this post, and also this book) (d) Shannon's channel capacity theorem, as shown by Yockey, provides a theoretical basis for understanding information transfer over many generations, and why evolution can work if it starts with an information-rich starting point rather than an information-poor starting point. Therefore, given the empirical these facts, you see that there are two possibilities - either evolution happens in a very limited fashion, evolution happens in a downward fashion primarily (de-evolution), or evolution happens according to pre-existing information. "Then demonstrate it empirically!" Oh, goodness. That's pretty much every experimental and theoretical study on selection. While the beneficial mutation rate is much higher than previously assumed (it was assumed to be lower because the idea of a teleological mutational mechanism never occurred to them), it turns out that selection against slightly deleterious mutations is problematic - it isn't strong enough to remove them. Kondrashov, for instance, points out that deleterious mutations which cannot be selected against represent a range of 4 orders of magnitude! In other words, in any reasonable population genetic scenario, you are going to primarily get de-evolution rather than evolution. To get beyond these results, you would have to propose a mutational system more radically teleological than what I'm suggesting. There's even a software system that allows you to test this at home. "Please explain the origin of *anything* from an intelligent design perspective without using the phrase “it was designed”." Why? Please explain the thermodynamics of *anything* without using terms such as "heat" and "energy". The point of ID is that agency is a fundamental, not a derived, cause (at least in relation to the other commonly-used fundamental causes). However, for a mathematical look at what design is (which might be what you are looking for), see this conference presentation.johnnyb_{August 19, 2012
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johnnyb,
I think it is, or at least the descendent of something designed (corrupted design is not problematic to ID, for instance).
Why is it that it has to be corrupted design? Is your method of telling "corrupted design" simply that the organism does something which you don't like? Perhaps you could give a few examples of designs that are still as the designer intended them to be and some which are not?
Finally, it is a conglomeration of multiple genes and introns and even DNA secondary structures that all contribute to this targeting. So, you would need all of these pieces simultaneously. Without them all simultaneously, the whole mechanism would be selected against.
But this is an argument that HIV is designed in it's current form. Given the difficulty that evolution has (as has been detailed here over the years) making even the simplest of changes I find it hard to understand from an ID perspective how a harmless organism could acquire the complex molecular machinery to become a deadly virus that can evade the immune system and medical technology.
(b) a descendent of an organism that wasn’t disease-causing. In other words, the design is deteriorating.
Not a very good design in the first place was it then? And if that's really the case then can this rate of deterioration be calculated? How?
Note that it is still true that purposeful mechanisms may have evolved, but, given the nature of the evolutionary process, it is likely that if they evolved, they evolved according to their programmed directions.
Why "is it likely"? So you want to have it both ways, even if it can be shown to have evolved then it evolved that way due to programmed directions. Given that we have the complete DNA sequences of many organisms now perhaps you could make a start on finding those "programmed directions"? Or you could say why you feel these "programmed directions" even exist all all other then to save your version of ID from irrelevance?
Perhaps the same reason everything isn’t 100% – because the design is deteriorating. This de-evolution is actually a much more empirically sound version of evolution that the Darwinian evolution which is often proposed.
Then demonstrate it empirically! If we look at the fossil record we don't see a pattern of deterioration. If we look at a bacteria over many generations we don't see a pattern of deterioration. The only "pattern of deterioration" we see is the one you invent to explain why HIV etc exists. Other then that, it's invisible.
The “where” is precisely what is both interesting and useful about the system, yet you think that it should be ignored in explanations of how it arose? I guess Darwinism turns ignoring evidence from an accident into a habit.
I quite agree. Please explain the origin of *anything* from an intelligent design perspective without using the phrase "it was designed".mphillips_{August 19, 2012
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Mung, Mutations being directed are the provenience of ID. Therefore it would be more relevant were you to show that they are directed, rather then placing the onus on others who are not making that claim. If you are genuinely interested on why it is generally accepted that mutations are random with respect to fitness then there is plenty of reading material out here. Furthermore, I would ask you how you would test a set of dice to see if they were "fair"? Is there any test that you can perform on the dice that would unequivocally show that they are not being directed? In your world, Maus, is there such a thing as a set of provably fair dice?mphillips_{August 19, 2012
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wd400 @33:
2. The somatic mutations you are talking about are not directed.
This has of course been established via empirical methods which you can cite.Mung_{August 18, 2012
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wd400:
3. You really don’t get the maths if you NFL has anything to say on evolution.
Huh?
In formal terms, there is no free lunch when the probability distribution on problem instances is such that all problem solvers have identically distributed results.
http://en.wikipedia.org/wiki/No_free_lunch_in_search_and_optimizationMung_{August 18, 2012
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wd400:
Biologists have done quite a lot of work in the last 2300 years, you might want to catch up…
I'm sure you'll be able to fill us in on the last 2300 years of progress by biologists.Mung_{August 18, 2012
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wd400:
Johnnyb, This is ridiculous. Evolutionary biology tells us how we can get apparent purpose as an a postori result of selection, without the requirement for goal-seeking by an organism or a designer. Just going from apparent purpose to design is begging the questions
If organisms are not goal seeking why are you posting here? Going from apparent purpose to no purpose is begging the question. wd400:
The somatic mutation system is not directed. That’s like saying the krebs cycle is teleological because it knows it’s going to get sugars at some stage.
The Krebs cycle is teleological. You're probably mistaken about WHY it is teleological. No surprise there.Mung_{August 18, 2012
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timothya -
It should be obvious that if a genome has an ability to hyper-mutate, then that ability will be expressed somewhere in the genome. The “where” is irrelevant to explaining why and how it arose. As a minimum, you have to explain why the capability to hyper-mutate inside somatic cells, and thereby generate non-heritable immune responses, is evidence of design.
See my response to mphillips above. Also, the "something had to happen, why not this?" argument is simply ignoring a large part of what we see - that what *did* happen correlates very heavily with function. In fact, you state at the outset that you are going to ignore the data:
The “where” is irrelevant to explaining why and how it arose.
The "where" is precisely what is both interesting and useful about the system, yet you think that it should be ignored in explanations of how it arose? I guess Darwinism turns ignoring evidence from an accident into a habit.johnnyb_{August 16, 2012
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mphillips - "So HIV is designed is it? It has a purposeful mechanism, wikipedia descirbes it as follows:" I think it is, or at least the descendent of something designed (corrupted design is not problematic to ID, for instance). "And it’s mutational strategy is to evade the human immune system and so far it’s done a fantastic job. So that strategy is obviously designed, as you show in this thread!" Exactly - glad you are catching on. Your more serious point is here:

In other words, if the mutations were focused merely somewhere else in the same gene, the necessary evolution would not happen.
Um, perhaps at one point they were and that organisms failed, leaving the fitter with the current configuration to survive.
But there are 3,000,000,000 base pairs, leaving 3,000,000,000 places to target. Perhaps you could get as small as 5,000,000 (since the target area is 600 base pairs wide - it would at least have to overlap the target region somewhat). In addition, it has to be timed right. In other words, mutating that region at the wrong time leads to failure as well. Finally, it is a conglomeration of multiple genes and introns and even DNA secondary structures that all contribute to this targeting. So, you would need all of these pieces simultaneously. Without them all simultaneously, the whole mechanism would be selected against. This is the problem of incipient structures which was first pointed out by Mivart.
Otherwise you get into the argument “well, why did the designer make things to infect you in the first place?”, as it seems a bit silly to give you an immune system that can’t cope with 100% of what’s thrown at it (or people would never die of infections or AIDS) and to keep inventing new things (directed mutations in HIVS) to throw at it.
Here you are getting beyond the bounds of current ID theory. ID can detect the design present in Stonehenge, but can't tell you why it was built. In addition, it can't tell you how many designers there are (perhaps HIV and other organisms had different designers?) But as a provisional answer, if you are indeed needing one, is that over and over again, most bacteria and viruses that cause disease are either (a) out of place ecologically (in other words, there is an ecological place where they function in a mutualistic situation), or (b) a descendent of an organism that wasn't disease-causing. In other words, the design is deteriorating. So why isn't the immune system 100%? Perhaps the same reason everything isn't 100% - because the design is deteriorating. This de-evolution is actually a much more empirically sound version of evolution that the Darwinian evolution which is often proposed. As I said, just like hearts have heart attacks, it doesn't mean that hearts don't have functions in the organism.johnnyb_{August 16, 2012
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JohnnyB posted: "You have missed the point – in the adaptive immune system, the place where the mutations are focused *is* the place where it is needed." I have to say that I think this idea is braindead. It should be obvious that if a genome has an ability to hyper-mutate, then that ability will be expressed somewhere in the genome. The "where" is irrelevant to explaining why and how it arose. As a minimum, you have to explain why the capability to hyper-mutate inside somatic cells, and thereby generate non-heritable immune responses, is evidence of design. Or more to the point, to demonstrate why this capability cannot arise via natural evolutionary pathways. You haven't done so, armwaving about Aristotelean "inferences" notwithstanding.timothya_{August 16, 2012
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johnnyb
In other words, if the mutations were focused merely somewhere else in the same gene, the necessary evolution would not happen.
Um, perhaps at one point they were and that organisms failed, leaving the fitter with the current configuration to survive. Otherwise you get into the argument "well, why did the designer make things to infect you in the first place?", as it seems a bit silly to give you an immune system that can't cope with 100% of what's thrown at it (or people would never die of infections or AIDS) and to keep inventing new things (directed mutations in HIVS) to throw at it. Not sure I like the sound of your "designer" so much TBH.mphillips_{August 16, 2012
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johnnyb,
Until you can re-establish their validity, common, uniform experience tells us that purposeful mechanisms are generally indicative of design.
So HIV is designed is it? It has a purposeful mechanism, wikipedia descirbes it as follows:
HIV enters macrophages and CD4+ T cells by the adsorption of glycoproteins on its surface to receptors on the target cell followed by fusion of the viral envelope with the cell membrane and the release of the HIV capsid into the cell.[35][36] Entry to the cell begins through interaction of the trimeric envelope complex (gp160 spike) and both CD4 and a chemokine receptor (generally either CCR5 or CXCR4, but others are known to interact) on the cell surface.[35][36] gp120 binds to integrin ?4?7 activating LFA-1 the central integrin involved in the establishment of virological synapses, which facilitate efficient cell-to-cell spreading of HIV-1.[37] The gp160 spike contains binding domains for both CD4 and chemokine receptors.[35][36] The first step in fusion involves the high-affinity attachment of the CD4 binding domains of gp120 to CD4. Once gp120 is bound with the CD4 protein, the envelope complex undergoes a structural change, exposing the chemokine binding domains of gp120 and allowing them to interact with the target chemokine receptor.[35][36] This allows for a more stable two-pronged attachment, which allows the N-terminal fusion peptide gp41 to penetrate the cell membrane.[35][36] Repeat sequences in gp41, HR1, and HR2 then interact, causing the collapse of the extracellular portion of gp41 into a hairpin. This loop structure brings the virus and cell membranes close together, allowing fusion of the membranes and subsequent entry of the viral capsid.[35][36] After HIV has bound to the target cell, the HIV RNA and various enzymes, including reverse transcriptase, integrase, ribonuclease, and protease, are injected into the cell.[35] During the microtubule-based transport to the nucleus, the viral single-strand RNA genome is transcribed into double-strand DNA, which is then integrated into a host chromosome.
Complex stuff, no? Too complex to have evolved? And it's mutational strategy is to evade the human immune system and so far it's done a fantastic job. So that strategy is obviously designed, as you show in this thread!mphillips_{August 16, 2012
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BTW, re "the necessary evolution would not happen", you do know that somatic mutations can't contribute to evolution... yes?wd400_{August 15, 2012
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No, I get your point, I just think it's, and this is really something, probably the stupidest argument I've ever heard for ID.wd400_{August 15, 2012
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wd400 - "The post is talking about the location of the mutations – they’re focused to particular places. They aren’t directed in the sense that the changes being made are the ones that are needed, which is what is meant by directed mutation in this thread." You have missed the point - in the adaptive immune system, the place where the mutations are focused *is* the place where it is needed. They are not only focused on the correct gene, but the correct *half* of the correct gene. In other words, if the mutations were focused merely somewhere else in the same gene, the necessary evolution would not happen. Now, if you are simply saying that the mutations are 99.99992% directed rather than 100% directed, then I agree totally. I just have to really wonder about an idea that disregards the 99.99992% and makes grandiose statements about the 0.00008% as if they were the main focus.johnnyb_{August 15, 2012
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The post is talking about the location of the mutations - they're focused to particular places. They aren't directed in the sense that the changes being made are the ones that are needed, which is what is meant by directed mutation in this thread.wd400_{August 15, 2012
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Hello Timothya,
Evolution, if true, will select mechanisms that are “purposeful” precisely because those mechanisms improve the fitness of the organism in relation to the environmental challenges it faces.
Evolution requires the existence of heritable recorded information, as well as the existence of a mechanism to transfer that information. Recorded information is properly disambiguated as form (i.e. the form of a thing) instantiated in a material medium. As such, it demonstrates material requirements. Our confidence in the existence and validity of these material requirements is supported by both their logical necessity, as well as their direct observation during the transfer. These physical requirements include two arrangements of matter; one acting as a representation of form in order to evoke an effect within a system (where the arrangement is necessarily arbitrary to the effect it evokes), and the second arrangement which serves as a transfer protocol (to materially establish the otherwise non-existent relationship between the representation and the effect). These two arrangements of matter form an (empirically and logically validated) irreducibly complex core which is fundamentally required in order to transfer recorded information (i.e. one is entirely useless without the other). These physical requirements also include the dynamic relationship between the two material arrangements just mentioned; that is, neither of them becomes the effect (i.e. the necessarily arbitrary relationship between the representation its material effect is preserved within the transfer by the protocol). Finally, the requirements include the production of unambiguous function in order to be identified (i.e. an arrangement of matter that does not produce a functional effect cannot be validated as ‘containing information’). People can say that such an irreducibly complex system (one that produces every single instance of biofunction observed on Earth) “does not have a purpose”, but then again, people can say anything. They do what profits them. Regarding your comment, the long and short of it is this: This system is not the product of evolution because evolution itself requires the system in order to exist. To say that evolution produced this system is to say that a thing that does not yet exist can cause something to happen - which is obviously false.Upright BiPed_{August 15, 2012
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timothya - "Evolution, if true, will select mechanisms that are “purposeful” precisely because those mechanisms improve the fitness of the organism in relation to the environmental challenges it faces." You say it will "select" them, but that assumes they are being generated. How do you know that evolution will generate them? This is precisely my point. For evolution to work, it must generate complex adaptations. Simply saying it will "select" them is silly - of course it will select them. But will it generate them? My contention, and what the evidence indicates, is that to the extent that it generates them, it is generated by predominantly purposeful mechanisms of mutations, not predominantly haphazard ones. "Presumably you mean that people believed this. So what? People in history have believed many things that are now evidently unture." But you missed my point. The reasons for thinking it untrue are no longer valid. Until you can re-establish their validity, common, uniform experience tells us that purposeful mechanisms are generally indicative of design.johnnyb_{August 15, 2012
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wd400,that article does say the SHM are 'tightly regulated' which permits the mutations to 'achieve a defined objective' and 'Chance is bounded by the limits of the system in which it operates'. Thus despite you assertion that the article does not say that the mutations are directed, the article is very clear that the mutations are 'tightly regulated' 'to 'achieve a defined objective'. Clearly you are defending a a-priori philosophical commitment to materialism rather than letting the evidence speak for itself. Why???bornagain77_{August 15, 2012
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JohhnyB posted this: "You are conflating several things – first of all, the purposefulness of the organism and the purposefulness of the evolutionary process. My point was that, contra the modern synthesis, the evolutionary mechanism itself is purposeful. As Larry Moran points out for us, the modern synthesis excludes purpose from the evolutionary process itself." I certainly do not conflate the two concepts. Evolution, if true, will select mechanisms that are "purposeful" precisely because those mechanisms improve the fitness of the organism in relation to the environmental challenges it faces. If you want to assign that "purpose" to a pre-existing "intention" then it is up to you to provide the evidence. And then posted this: "Prior to natural selection, purposeful mechanism was indicative of design." Presumably you mean that people believed this. So what? People in history have believed many things that are now evidently unture. To whit: the authors of the Christian Old Testament.timothya_{August 15, 2012
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