Biologos, Venema and the Scientific Imagination
| September 15, 2011 | Posted by Steno under Intelligent Design |
Denis Venema wants to explain evolution to evangelical Christians because he doesn’t think it is understand sufficiently. But he asks us to use our imagination and avoids a carefully modelled defence of evolution. If that is the best Darwinists can do then is it any wonder that many of us reject it? See:
Venema Understanding Evolution: An Introduction to Populations and Speciation
Firstly, Venema follows the common evolutionary practice of presenting evidence for evolution by focussing upon the micro changes and then extrapolating without evidence to the macro evolutionary scale by assuming it happens by similar means. But the micro changes, such as that of his exampled stickleback fish, are simply uncontested even by young earth creationists, but what is contested is the belief that we can move from the small to the big without developing and modelling a credible pathway. Time and again evolutionists fail to deal with the problems, but simply make the switch from small to big thinking the flaws in their reasoning will not be noticed.
Venema though asks us to use our imagination to understand evolution. I find that wholly inadequate scientifically, especially when we can model such claims mathematically. And I wonder why such imaginary thinking has a right to be called science. He does though present claims that can be questioned scientifically; for instance believing that humanity evolved within a population size of roughly 10,000 people. So how should we model these claims?
Assuming 20 years for a generation and 6 million years from an ape-like ancestor to mankind would give 300,000 generations to achieve an evolutionary progression from an ape-like ancestor to man. As an aside, in that time only 3 billion individuals would have lived and died, a smaller number than the present human population alive today. Does he really expect us to believe that man could have arisen in so small a number of ancestors? Presumably we can look at the incidence of beneficial mutations in the present human population and ask whether sufficient beneficial mutations would have arisen and be compounded through 300,000 generations. I am afraid it doesn’t look good for evolution.
So down to modelling; we are led to believe that there is 1 percent difference between ape and man in the 3 billion base pairs of DNA, and if we use unrealistic assumptions then we might assume only 10 percent of DNA is coded with the rest considered ‘junk.’ But even 1 percent of 300 million is 3 million nucleotide differences between ape and man.
So we have to find 3 million base-pair beneficial mutational changes in 300,000 generations, or 10 per generation, both found and fixed in the population per generation. Is that possible? I challenge anyone to tell me it is adequate from what we know about the way the present day human population finds and fixes beneficial mutations, even for instance on a small island community of 10,000 people. It comes up against a number of problems.
Problem1. Haldane’s dilemma as discussed by ReMines in The Biotic Message and Sandford in Genetic Entropy (Refs below) (One might have thought these books would be at the top of Venema’s reading list considering his position). Anyway, as a simple overview of the claims of these books, in order for beneficial mutations to be fixed in the population we would need to pay a cost in terms of survivability of the mutated offspring against the un-mutated ones. Haldane thought it as high as 30 to 1, and higher vertebrates cannot hope to pay that cost. Haldane thought a cost of 0.1 per generation might be affordable and that it would take 300 generations to fix 1 beneficial mutation in a population. Venema’s population might then fix 1000 beneficial mutations in 6 million years; a little short of the 3 million required.
Problem 2. We may also ask whether beneficial mutations actually provide any selective advantage to an organism. Sandford for instance has pointed out that beneficial mutations, when they rarely occur, are virtually invisible at the level of the phenotype anyway and so even Haldane’s 0.1 per generation looks unlikely.
Problem 3. Harmful mutations are far more common than beneficial ones, perhaps as high as 1000 to 1. In order to weed out the harmful mutations evolution would have to proceed at a very slow rate indeed so that error catastrophe doesn’t occur in the population; a problem known today where small inbreeding populations are often on the verge of extinction. Furthermore, small populations do not have sufficient resources to find the necessary beneficial mutations, even though it makes it easier to spread the mutations that do occur through a population. A large population is more likely to find beneficial mutations, but work against their spread through the population due to the size.
So in summary, I would challenge Venema to respond seriously to the questions raised by Sandford and ReMine.
Sources: Walter ReMine’s The Biotic Message, St Paul, Minnesota: St Paul’s Science, pp. 208-236. Sanford, J (2005) Genetic Entropy and the Mystery of the Genome, New York: Elim Publ, especially pp.159-160, Haldane JBS (1957) ‘The Cost of Natural Selection,’ J. Genetics 55:511-24.
85 Responses to Biologos, Venema and the Scientific Imagination
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I chuckled at this one. You lead with:”Denis Venema wants to explain evolution to evangelical Christians because he doesn’t think it is understand sufficiently” and as if to prove his point, you proceed to butcher the topic.
Your assumptions:
1) 10 percent of DNA is coded with the rest considered ‘junk.’ (way high)
2) 3 million base-pair beneficial mutational changes (Beneficial???)
Could you explain your logic on these mutations ALL being beneficial? Really, I’m curious. Do you think only beneficial mutations can fix?
In contrast to your approach, let’s just take the simplest route, and say that on average, the across the genome mutations are neutral. Under neutral selection, the rate of fixation for a mutation not subject to selection is the rate of introduction of such mutations. A low estimate is ~1.1×10?8 per site per generation. Times 3 billion sites, 300,000 generations, 2 lineages, we’re at 19.8 million, or 1.51%.
Not bad. Of course, functional sites show purifying selection, so fewer mutations get fixed there then elsewhere, and open reading frames end up showing ~99.5%+ identity-that is, about 30% of human and chimp proteins having identical amino acid sequences, and the remainder having one or two differences. Are even all these beneficial? Probably not. Some of those tested seem to do little functionally. Many are nearly synonymous, substituting a very similar amino acid.
By the way, this difference is only about 10 times the difference between any two humans, if I recall correctly.
Haldane’s dilemma has been dealt with extensively elsewhere.
Instead of DrREC’s grossly misleading hypothetical scenarios for the neo-Darwinian evolution of humans, let’s look at some actual evidence and see what reality itself is telling us about the plausibility of neo-Darwinian evolution of humans. First no neo-Darwinists seems be able to show me ANY beneficial mutations, in humans (or anything else for that matter), that will withstand scrutiny, (Lactase persistence, and Himilaya high altitude/low oxygen tolerance mutations, in humans, both fail scrutiny for functional information generation, much less can the mutations be claimed as purely random mutations and not, in fact, be claimed as ‘calculated’ mutations), Yet the evidence for detrimental mutations in humans is simply overwhelming:
I went to the mutation database website cited by John Avise and found:
I really question their use of the word ‘celebrating’. Using real world parameters, here is the correct model for what is actually going on with genomes:
Here is a pretty accurate measure for the detrimental mutation rate in humans.
This ‘slightly detrimental’ mutation rate of 60, per generation is far greater than even what neo-Darwinists agree is a acceptable mutation rate for an organism:
etc.. etc.. etc..
To show how grossly misleading neo-Darwinists can be about population genetics, on the web and to the general public, here is the neo-Darwinists very own population genetics model applied to the hypothetical scenario for whale evolution;
Moreover, despite what DrREC, and other neo-Darwinists on the web may say, the fact that there are severe problems in the mathematical population genetics model of neo-Darwinists is readily admitted by many of the population geneticists themselves:
But, of personal note, when considering the multiple overlapping layers of coding in the genome,,,
,,,I simply find that it is beyond ludicrous to even begin to entertain the thought that this level of unmatched functional integrated information was put together by mutations filtered by differential death. But alas, as Dr. Hunter says, ,,, Religion drives science and it matters!
Moreover, neo-Darwinism is simply at a complete loss to explain the beauty of this:
Standing Ovation! Jackie Evancho WOW’s Audience! – Inspirational Videos
http://www.godtube.com/watch/?v=KK67Y7NX
If it’s one thing I hate with a passion its the low probability but great amount of time argument. If everyone is honest we will realize that this is a very difficult problem where small mistakes in measured rates have great consequences.
Two examples from basic math
The harmonic sequence
1/1 + 1/2 + 1/3 + 1/4 …. so many terms , but each gets smaller. What is the answer? – it never stops growing and can be shown to be infinite ( or more technically, non-convergent.(
A power series
9/10 + 9/10^2 + 9 /10^3 + 9/10^4… This again has an infinite number of terms, but it not only converges but has a recognizable answer. It is the number that is usually written 1. ( one ).
In order to make real quantitative arguments about probabilities or sequences involving a large number of trials with small probability, you have to know the detailed quantities to incredible precision. Hand waving arguments which move from micro evolution to macro evolution are just so much garbage.
Initially it may have seemed the more “scientific” option to be a naturalist. However as soon as the naturalist endeavors to defend their belief they are constantly defying “science” at every turn.
How can a “scientist” look at a whole system that is slowly by short and sure steps degrading, go and tell the world that it is evolving?
Imagination is key I suspect.
One day there was a single celled organism splooshing around all by itself having all sorts of fun. It was the only life in the whole universe. I cant tell you how it got there.
He was lonely so he turned into two organisms. I cant tell you how. He wished he could turn into a bird and fly in the sky so he did. Don’t worry its not magic coz it took a real long time for him to do it.
Wow! thank you imagination I now understand the theory of evolution.
Semi OT:, In this podcast, Casey Luskin thoroughly debunks the hype surrounding the newest missing link, Australopithecus sediba. Starting a little after the 7:00 minute mark on the podcast, he quotes from several leading paleontologists in the field who express deep skepticism for the grandiose claims being made in media headlines about its status as irrefutable proof of a ‘missing link’ for human evolution:
Recently Reported Fossil is Old News: Media Hype & the Upcoming Election
http://intelligentdesign.podom.....6_16-07_00
“much less can the mutations be claimed as purely random mutations and not, in fact, be claimed as ‘calculated’ mutations)”
Haha…there it is. Show BA77 evidence of a gain-of-information mutation, and guess what, it is designed. How was this detected, how do you discern it from natural processes?
Doesn’t matter-because design is just something you can tack onto any observation. It is unfalsifiable in this sense. See something evolve-thats just design unfolding.
Which is fine as a personal belief. It is also more simply called theistic evolution. It isn’t much of a science.
Anyone want to show calculations that the number of mutations between humans and chimps is impossible?
Anyone want to defend the claim in the original post that there must be a whopping number of beneficial mutations?
DrREC actually, to show you for the inflexible/dishonest neo-Darwinian dogmatist that you truly are (which I enjoy doing by the way), here is the clear evidence, in the Himalayan oxygen mutation, that throws up a huge red flag on such mutations being considered truly random mutations, as is required by neo-Darwinism (your religion), and clearly points to the fact that they should in fact be considered ‘designed/calculated’ mutations arising ‘rapidly’ from the regulatory epigentic information controlling the DNA:
Further notes:
DrREC, do you want to show ANY evidence that just one gene and/or protein can arise by neo-Darwinian processes?
Could Chance Arrange the Code for (Just) One Gene?
“our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
http://www.creationsafaris.com/epoi_c10.htm
“Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: – Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.”
http://www.mendeley.com/resear.....yme-folds/
“DrREC, do you want to show ANY evidence that just one gene and/or protein can arise by neo-Darwinian processes?”
Recent de novo origin of human protein-coding genes
http://genome.cshlp.org/conten.....095026.109
Evolution of novel genes.
http://www.ncbi.nlm.nih.gov/pubmed/11682312
Strategy and success for the directed evolution of enzymes.
http://www.ncbi.nlm.nih.gov/pubmed/21684150
“……including examples of catalytic activity for which there is no precedent in nature”
This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 ‘ORFan’ genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!
The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true.
This following site has a brief discussion on the biased methodology of the preceding study:
http://www.uncommondescent.com.....ent-358505
If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:
In fact it turns out that the authors of the ‘kick the ORFans out in the street’ paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias:
http://www.uncommondescent.com.....ent-358547
Moreover the ‘anomaly’ of unique ORFan genes is found in every new genome sequenced:
As well, completely contrary to evolutionary thought, these ‘new’ ORFan genes are found to be just as essential as ‘old’ genes for maintaining life:
of related interest:
Why DrREC, so all you have to do to prove your point is say that Protein a evolved from protein b??? Why that is just special DrREC! Perhaps you could sooth my doubts and actually physically demonstrate the origination of a new protein from a old protein and establish your theory/religion as at least scientifically plausible???
BA77, they aren’t limited in red blood cell production.
Read the article: “What’s unique about Tibetans is they don’t develop high red blood cells counts”
Which is a good thing. Google polycythemia and thrombosis if you don’t believe me. Increased blood viscosity risks clots, spleen damage, etc.
They have heathy hematocrit values–not exactly a loss of information, or deleterious mutation. What is remarkable is they harbor adaptive mutations to a number of genes, that allow them, without cranking out massive numbers of red blood cells, to survive at elevation. These are gain-of-function mutations, despite your blustering otherwise.
Many more recent publications:
http://scholar.google.com/scho.....8;as_vis=1
“Why DrREC, so all you have to do to prove your point is say that Protein a evolved from protein b??? Why that is just special DrREC! Perhaps you could sooth my doubts and actually physically demonstrate the origination of a new protein from a old protein and establish your theory/religion as at least scientifically plausible???”
I’m sorry, I find this rant awfully incoherent, and I don’t understand why my previous references are insufficient to answer your query.
The first two demonstrate the generation of novel, functional proteins by mutation and recombination of previously non-coding regions. The last demonstrates the directed evolution of novel activities (taking activity/protein a and evolving it into activity/protein b, where b doesn’t exist in nature, by ‘Darwinian’ processes-mutation and recombination acted on by selection.
DrREC, you got to be kidding, do you actually think your last paper that you cited is neo-Darwinian in the least. Those guys are using every bit of knowledge and ingenuity they got to ‘intelligently’ direct the experiment. Perhaps you don’t consider the experimenters intelligent since they are merely accidental by-products of Darwinism and thus it is okay for them to interfere with neo-Darwinian processes as much as they wany??
But as for myself, I see a very heavy thumb on the scale for your supposed evidence that testifies all the more clearly of the poverty of your evidential base since you have had to resort to such shenanigans!
” ‘intelligently’ direct the experiment”
No, they don’t design the outcome. They generate variation with mutation and recombination, and select for results. How is this not analogous to natural selection?
DrREC you claim:
‘The first two demonstrate the generation of novel, functional proteins by mutation and recombination of previously non-coding regions.’
Excuse me, they infer relationship from sequences and definitely do not DEMONSTRATE the novel proteins arising!!!
So neo-Darwinian evolution practices,,, Strategy and success for the directed evolution of enzymes
Calling a AMC Gremlim a formula one race car does not make the it true DrREC, But alas truth is not what you are interested in is it???
LOL, so now we’re down to direct observation, and the rejection of inference.
Have you observed design, or is it an inference?
DrREC, why don’t you use the Lenski Long Term Experiment to DEMONSTRATE what almighty neo-Darwinism can do??? Oh that’s right Lenski’s e-coli support the opposite conclusion!
The query wasn’t limited to natural processes. It was for the origination of a novel protein by ‘Darwinian’ processes. Recombination and mutagenesis coupled with selection made novel proteins.
DrREC, you are the one who said DEMONSTRATE, I merely exposed you for being a liar once again to cover up the fact you have ZERO evidence!
But we could do this forever. BA77, regarding the original thread:
Want to show calculations that the number of observed mutations between humans and chimps is impossible?
Want to defend the claim in the original post that there must be a whopping number of beneficial mutations?
“DrREC, you are the one who said DEMONSTRATE,”
“Excuse me, they infer relationship from sequences and definitely do not DEMONSTRATE the novel proteins arising!!!”
Whatever. Calm down.
As for the evidence in that paper-why reject the inference. Non-coding sequences in present in other species have a mutation or recombination yielding a functional protein in one. They have been tested for function. Conclusion-evolution of a novel, functional protein.
You reject this as a inference. Have you observed design, or is it an inference?
DrREC, ‘The query wasn’t limited to natural processes.’
Hmm the exact point being debated wasn’t used. How special!
DrREC, you do not seem to grasp the most fundamental point of empirical science. For you to support your delusional claims for neo-Darwinism, you must actually demonstrate the origination of genes and proteins by purely neo-Darwinian processes. You cannot assume the conclusion you want to make in your argument, by merely alluding to sequence similarity. It is the very point being debated and is not satisfied by anything less than a actual demonstration.
DrREC, I’ve shown papers (Axe; Behe) that DEMONSTRATE the neo-Darwinian evolution of proteins and genes, that are completely different between chimps and man, is impossible. Whereas you have merely shown a preconceived conclusion imposed on sequence similarity data. As far as science is concerned experiment beats conjecture all the time, thus the burden is on you.
DrREC you ask:
DrREC, any time you, or anyone else posts a comment, I confidently observe design in action. The reason I can be confident that design is involved is that when you generate the functional information in your comment you post, you have in fact exceeded what is possible for the entire material processes of the universe over the entire history of the universe. Since I know of ZERO instances of neo-Darwinian evolution DEMONSTRATING the generation of that level of functional information, then the inference holds. Whereas you on the other hand are inferring something that has NEVER been demonstrated for neo-Darwinian evolution, must less purely material processes,, namely the generation of a ‘non-trivial’ level of functional information:
DrREC, you might as well give up the argument. This fool will be satisfied with nothing less than one of his precious youtube videos of a beneficial protein-coding mutation arising in real time, complete with sound effects and laser light shows. On the other hand, he is perfectly willing to accept the slightest hand wave in the direction of
divine interventiondesign.I think the operative phrase is “selective hyperskepticism”?
“He does though present claims that can be questioned scientifically; for instance believing that humanity evolved within a population size of roughly 10,000 people. So how should we model these claims?
Assuming 20 years for a generation and 6 million years from an ape-like ancestor to mankind would give 300,000 generations to achieve an evolutionary progression from an ape-like ancestor to man. As an aside, in that time only 3 billion individuals would have lived and died, a smaller number than the present human population alive today. Does he really expect us to believe that man could have arisen in so small a number of ancestors? ”
–There were about 1 billion people in 1800. All of those people were dead by 1920, when the world population was 2 billion – and now just about all of those people have died. There’s your previous 3 billion people – just right there. So obviously more than 3 billion people have lived and died in the previous 6 million years.
Denis Venema wasn’t saying that humans only numbered about 10k throughout our history. He said that humans never numbered LESS than 10k, and he said it in context of explaining that it’s POPULATIONS that evolve, not individuals. And thus his point is that the “first” humans were a population of at least 10k – and so evolution doesn’t claim that there was ever a “first human” or “first pair” of humans. And this was just the initial population size.
The estimates I usually hear is that pre-agricultural revolution that humans were a roughly stable population of about 1 million, and that over 100 billion humans have lived and died. Those are roughly the numbers mentioned here:
http://en.wikipedia.org/wiki/W.....ever_lived
Prof. FX Gumby, perhaps you can entertain ‘this fool’ with a actual DEMONSTRATION of neo-Darwinian evolution generating genes/proteins, instead of just sequence similarity comparison that presupposes the very thing being asked into its conclusion???. Shoot Prof. FX Gumby, let’s just get all silly, clown-like, foolish and look at the 50,000 generations of e-coli in the Long Term Evolution Experiment of Lenski, which is equivalent to about a million years of supposed Human evolution, since it is the best direct evidence we got for the power of Darwinism, and see what the almighty power of neo-Darwinian evolution has DEMONSTRATED for this fool to behold:
And the drum-roll please,,,,,,,
But that can’t be right Prof. FX Gumby,,, the mutations interfered with each other, preventing further ‘evolution’, so let’s take a closer look,,
Prof. FX Gumby, this is not good for you guys. Perhaps if you insult us fools who question the almighty power of Darwinism a little more, then you can make these consistent types of experimental results magically go away. But then again something tells me this is NEVER going away!
Prof. FX Gumby,
I wouldn’t be too harsh. I think bornagain77 summarizes the ID position well-no one here seems to ever correct him. His posts are revealing.
Since functional information DOES increase in directed evolution, natural evolution, and genetic algorithms (even Behe lists “adaptive gain of functional coded elements)” in his latest review, what are we left with?
BA77 provides the answer–in the face of observations that show the pathways (mutation and recombination) by which the novel activities can about, he sees design.
This is trick one: “purely neo-Darwinian processes” Purely? How do I prove that? How do I rule out the influence of a designer in human evolution, or my test tube. I can’t. Maybe the designer came in and did something. I can describe the process, the natural process that fully accounts for it. But he sees design, and declares it. No detection, no scientific need to invoke it, but there it is. This makes ID a non-falsifiable equivalent of theistic evolution. See the natural process, study the process, but it must have been guided. What’s the difference?
Trick two is using the evidence only when it is helpful to ID: “they infer relationship from sequences and definitely do not DEMONSTRATE the novel proteins arising”
So sequence based-inferences ala the original post, Behe, etc., are fine, but when the evolution of a new gene by comparing humans and chimps is inferred, we must strike it from the record. Very convenient.
Trick three is resorting to hocus-pocus interpretations of science. The quantum mechanics business is a good laugh. Hey BA77, you never answered my question: does ‘realism’ have the same meaning in quantum mechanics and metaphysics? Until you figure out that one, you’re pretty much embarrassing yourself here.
DrREC you state:
First, let’s look at your example for ‘directed’ evolution. From their abstract in the paper we find this quote
DrREC, perhaps you find designing strategies to overcome the dead-ends of neo-Darwinian processes to be a purely neo-Darwinian process, but DrREC the last time I checked designing strategies was held to be a intelligent activity. i.e. you are severely begging the question by claiming this paper as proof for what neo-Darwinism can do.,,, DrREC, you then claim ‘natural’ (purely Darwinian) evolution can produce functional information; Well since this is the very point being debated now we are getting somewhere. But alas you have provided no paper showing Darwinian evolution producing any non-trivial functional information (genes and/or proteins) where as I’ve cited Lenski, Behe, and Axe that shows that there are severe limits for what neo-Darwinian processes can do. Thus apparently you think your word that it can happen by purely neo-Darwinian processes is good enough to establish your claim beyond reasonable doubt, but alas I do not trust you. In fact I think neo-Darwinists, by and large, are a very dishonest people! Thus please present the exact empirical evidence instead of just your say so that it is so. You then claim that genetic algorithms, which are designed by humans, can create functional information. But when these man-made genetic algorithms are looked at closely we find:
Thus DrREC, do you concede the main point of Dembski’s paper, that IF neo-Darwinism could generate functional information in life, (which no empirical demonstration has been forthcoming by neo-Darwinists that it can do as such, which is the main point being debated by the way), that that gain in functional information would have to be the result of Intelligent Design built into nature??? Then DrREC, you have the sheer audacity to actually cite Behe’s latest paper as proof for neo-Darwinian evolution. I think Eric Anderson addressed this quite well on Gil’s post:
You then go on to state I’m being unreasonable in my view of the evidence for discounting your ‘strategies for success’ paper, which clearly, as illustrated earlier, is ‘designed’ to overcome neo-Darwinian dead-ends. But alas DrREC, why do you want this paper to count for neo-Darwinism so badly when, clearly, to reasonable people, it does not count as a purely neo-Darwinian process? It is because, as empirically DEMONSTRATED with Lenski’s e-coli and Behe’s malaria and HIV, you have no evidence, whatsoever, that purely neo-Darwinian processes can do anything beyond the utterly trivial as far as generating functional information above and beyond what is already present in life!!! You then gripe about my discounting of the sequence similarity evidence you cited as ‘proof’ of neo-Darwinism, which once again clearly shows that you have no grasp, whatsoever, of the most fundamental precepts of empirical science, for clearly you have not DEMONSTRATED that proteins can change from one remote island of functionality to another remote island of functionality by neo-Darwinian means, but have merely asserted the very point being questioned does not have to be demonstrated. i.e. neo-Darwinists need to show the step by step amino acid substitution process by which proteins make these universe wide leaps to different islands of functionality (Axe; 2004) without ending in failure for the functionality of the protein!!!
DrREC, You then go on to have a ‘good laugh’ at this ‘quantum mechanics business’. But alas the last laugh is on you for quantum mechanics, due to recent breakthroughs in science, has falsified the ‘reductive’ materialistic theory of neo-Darwinism:
DrREC, I actually had a neo-Darwinists tell me the other day that none of the preceding evidence matters to neo-Darwinism for neo-Darwinism does not care about material particles or quantum entanglement/information, but only cares about how species change over time. To which, it may surprise you to find, that I whole-heartily agreed with him. For I told him that, as far as I could see, neo-Darwinism has nothing, whatsoever, to do with how reality is constructed at all!!
DrREC, here is some more that ‘quantum business’ for you to get a ‘good laugh’ with:
As Professor McIntosh points out in the preceding video, information is a very elusive entity to nail down, for though we can write it down, encode it, and transfer the information from one material medium to another completely different material medium, the information never changes its meaning though the material mediums, on which the information is stored, are completely different upon the information’s transfer.,,, It is also interesting to note that a Compact Disc crammed with information on it weighs exactly the same as a CD with no information on it whatsoever.,, i.e. Information, from our everyday experience, gives every indication of being completely transcendent of any material basis. i.e. Information gives every indication of being ‘real’ and yet it also gives every indication of being transcendent of time and space though it may be stored on various material mediums. Moreover, although our everyday experience gives us a very enigmatic picture of ‘information’, breakthroughs in quantum mechanics have given us a more complete picture of ‘information’ and its place (prominence) in the overall structure of reality; Anton Zeilinger, a leading researcher in Quantum mechanics, gives a brief outline, of how quantum entanglement/information is extended to allow quantum teleportation, in this following video;
And quantum teleporation shows that atoms, which are suppose to be the basis from which functional information ‘emerges’ in the neo-Darwinian framework, are now shown to be, in fact, reducible to the functional information that the atoms are suppose to be the basis of!
i.e. It is impossible for quantum information/entanglement to ever ‘emerge’ from any material basis of atoms when atoms are now shown to reduce to a transcendent basis of quantum information in the first place!!! But alas DrREC, I’m fairly certain that none of these insurmountable problems for the reductive materialistic framework of neo-Darwinism presented by quantum mechanics matters to you, and that you will have another ‘good laugh’ at all that ‘quantum business’. But, if you do do as such, then to me it just demonstrates once again your intellectual dishonesty to the facts and your dogmatic belief in neo-Darwinism no matter what the evidence says to the contrary;
Further note:
There still isn’t any genetic evidence that demonstrates the changes required (from chimp to human) are even possible.
So you have to start there. Good luck…
DrREC:
Nope, nothing about Darwinian processes there- just question-begging.
Not one link supports the claim that Darwinian processes didit. Strange…
DrREC,
All you are doing is engaging in question-begging- Just how was it determined that gene duplication and recombination are ‘Darwinian’ processes?
Do you realize that ID is not anti-evolution? Or do you really think your ignorance refutes ID?
Would the Darwinists among us care to comment on the points BA77 highlighted relating to Lenski’s 50,000 generation e. coli experiments, which would equate to about 1 million years of human evolution.
In particular the points raised in comment 12.1. Quite revealing in it’s findings, but perhaps I’m missing something.
Well, a quick comments from me:
ba77 wrote:
It isn’t “equivalent to about a million years of supposed Human evolution” because bacteria are cloning species, not sexually reproducing species. This makes a huge difference.
It’s not the only problem with ba77′s point, but it’s an especially glaring one.
Actually, there’s a sense in which bacteria aren’t “species” at all. They aren’t by most definitions.
I’m unable to find Axe or Behe mentioning the evolution from ape to man being impossible.
Are you quoting them or making an inference?
“Just how was it determined that gene duplication and recombination are ‘Darwinian’ processes?”
I really now don’t know how much extra meaning you’ve loaded into ‘Darwinian’ but mutation, gene duplication and recombination are well-examined natural processes.
Are you trying to say I can’t prove they are natural, that perhaps a designer is using them in executing designs?
Fine. I can’t falsify that. Keep it as a personal belief. This leads me to the answer of your second question. I do NOT think ID is anti-evolution. I think it has degraded to theistic evolution.
Well, no, ba77, and Lenski himself doesn’t think so.
DrREC:
Design is a natural process too- a well-examined natural process.
But anyway you don’t have any evidence taht gene duplication and recombination are blind, undirected chemical processes- ie darwinian processes.
As for ID and theistic evolution- well ID is nothing like TE.
Well by golly Elizabeth, if bacteria have nothing to do with human evolution then I guess the entire Random Mutation and Natural Selection process itself has absolutely nothing to with Human Evolution either!!!! Too bad I know your playbook Elizabeth,,,, i.e. neo-Darwinian tactic #5, when faced with clear evidence that severely contradicts neo-Darwinism, deny that the clear evidence has anything whatsoever to do with evolution.
Elizabeth, you have to be completely blind, or hopelessly dishonest, to not see HUGE problems for neo-Darwinism in this evidence.
Further notes:
Nice non-sequitur. You do realize that ID is not anti-evolution…
Yes it does make a huge difference and that difference argues against universal common descent as sexual reproduction put an end to it.
Well Elizabeth, since I’m more interested in what the e-coli experiment actually says, than what Lenski personal opinion is, I think I will follow the evidence and not a dogmatic personal opinion of a scientists that refuses to acknowledge the clear implications of the evidence, even when that evidence is right before their very eyes. In fact, this experiment kills two birds with one stone, 1. It demonstrates the extreme difficultly, faced by neo-Darwinian processes, to locate random mutations that will actually work together to build functional complexity/information, i.e. to actually evolve something,,, and 2. it demonstrates the extreme blindness that Darwinists have to any results that contradict their deeply held beliefs in neo-darwinism, even when those findings are wrought by their very own hands.
Not at all, ba77, but sexual reproduction provides a very different and much more efficient mechanism for propagating potentially useful alleles through a population, because DNA sequences can “travel” independently.
However, rather than bother to find out whether I might have a point here, you cast aspersions on my motives.
I suggest you find out a bit more about how alleles propagate through sexually reproducing populations before you generalise findings from bacterial studies to humans, or even to fruitflies,and certainly before you accuse the people who take issue with your conclusions of “blindness”.
No, it doesn’t “argue against common descent” (or at least you aren’t making the argument that it does).
Elizabeth you state:
You are right, it is a extremely bad insult to people who are actually blind to compare them to the dogmatic neo-Darwinists whose ‘blindness’ is, as far as I can tell, a matter of personal religious preference rather something beyond their control, thus my apologies to all actually blind people reading this!
Of note:
So I take it you are going to find out why sexual reproduction makes a difference to the rate of adaptation in terms of generations?
Elizabeth you also state:
Well Elizabeth since you seem to think you have population genetics all figured out, I suggest you apply for the job at Oxford University to straighten the problems of population genetics out;
as to
It seems even population geneticists themselves admit to the severe deficiency of neo-Darwinian mechanisms to account for such:
But alas Elizabeth, this is merely mathematical models, so let’s look at the ‘real’ world, at the experiments on fruit flies (something you accused me of ignorance on), and see if we can find evidence for ‘alleles propagating’;
But hey Elizabeth, you say that sexual reproduction solves all this, whereas I, nor apparently population geneticists or experimental biologists, can find any evidence that it does anything of the sort. But just curious Elizabeth, can you please tell me, in purely neo-Darwinian terms, how sexual reproduction came to be in the first place???
Shoot Elizabeth, can you please give me a clear neo-Darwiniam pathway as to how self-replication started in the first place???
Shoot Elizabeth, can you give me a clear neo-Darwian pathway as to how ANY molecular machine whatsoever came to be???
Thus apparently Elizabeth, neo-Darwinists have ZERO evidence for the claims you are making. The sheer poverty of evidence for such sweeping claims as to how life came to be on Earth, should stop neo-darwinism dead in its tracks, but alas, as Dr. Hunter says, its not about the science, it’s about Religion;
I’m interested in how the slow change in some bacteria comports with ba77′s views on genetic entropy.
Does the designer arbitrarily prevent prevent change, or does he only do this for spore-forming bacteria?
Yes, it does. Ya see with sexual reproduction even the most beneficial mutation may not even make it to the next generation as only 1/2 of each parent’s genome makes it. And it doesn’t have to be the 1/2 with the beneficial mutation.
As geneticist Giuseppe Sermonti said:
(snip a few paragraphs on peppered moths)
Semi OT; Casey Luskin’s excellent follow up article debunking Australopithecus sediba’s exalted status, in mainstream media, as a missing link;
Sexual reproduction will only slow the rate, if not kill it.
Well, Sermonti has ignored drift.
as to:
to which it can only be observed
To which I could observe: nope, Joseph and ba77 are ignoring reality.
But it wouldn’t get us very far, would it?
I suggest both of you read a little more widely on the population genetics of sexually reproducing populations.
Well Elizabeth since you claim you are NOT ignoring reality, let’s just conduct a little experiment and observe, once again, just a little bit about how reality is actually constructed, and how it relates to life, and how it falsifies the materialistic framework of neo-Darwinism, and see if you will ignore how reality is constructed, once again, just so as to preserve your blind faith in your atheistic form of neo-Darwinism; i.e. your chosen religion!
First, as to ‘spatial relations’ of reality, I noticed that in this following video, on the optical effects for a observer approaching the speed of light, that the 3- Spatial Dimensions, we currently live in, ‘folded and collapsed’ into a tunnel shape, around the direction of travel, as the observer approached the constant of the speed of light.,,,
Here is the interactive website, put together by two Australian University Physics professors, which is directly related to the preceding video, which has a link to the relativistic math on it at the bottom of the page;
Please note the ‘light at the end of the tunnel’, at the 3:22 minute mark of the preceding video, which uncannily matches very many of the Judeo-Christian Near Death Experience testimonies of western cultures;
Also of related note to how the 3-Dimension world folds and collapses into a tunnel shape, as the ‘higher dimension’ of the speed of light is approached, is the ‘eternality of time’ revealed by the time dilation of special relativity.
This higher dimension, ‘eternal’, inference for the time framework of light is warranted because light is not ‘frozen within time’ yet it is shown that time, as we understand it, does not pass for light.
But since the material particles, of the person’s body who is having a Near Death Experience, are clearly ‘staying behind’ as the person is having the Near Death Experience, then, of course, the consciousness of the person must be based on something other than the material particles of the body. Something that must be transcendent of the material realm. (Also of interest to this, as the Cern Particle Accelerator readily testifies, it is not ‘natural’ for material particles to approach the speed of light and, indeed, takes a massive amount of energy for even sub-atomic particles to closely approach the speed of light.) This transcendent something, on which human consciousness must actually be based, instead of ‘emerging’ from the material particles, is found to be ‘quantum information’. Transcendent Quantum Information is now shown, empirically, to be foundational to the human body here:
Whereas, quantum information is strongly implicated in human consciousness here:
Particular quote of note from preceding video;
Corroborating experimental evidence here:
And quantum information is conclusively shown to be transcendent of any material basis here:
The falsification for local realism (reductive materialism) was recently greatly strengthened:
This following video reveals just how downright ‘spooky’ (to use Einstein’s description) quantum entanglement is:
And quantum information is shown to be ‘conserved’ here;
Of related note; I really enjoyed Michael Egnor’s essay on how consciousness is not reducible to matter;
more notes of interest:
Whereas, quantum information is strongly implicated in human consciousness here:
Particular quote of note from preceding video;
Corroborating experimental evidence here:
And quantum information is conclusively shown to be transcendent of any material basis here:
The falsification for local realism (reductive materialism) was recently greatly strengthened:
This following video reveals just how downright ‘spooky’ (to use Einstein’s description) quantum entanglement is:
And quantum information is shown to be ‘conserved’ here;
Of related note; I really enjoyed Michael Egnor’s essay on how consciousness is not reducible to matter;
more notes of interest:
whoops wrong spot:
Whereas, quantum information is strongly implicated in human consciousness here:
Particular quote of note from preceding video;
Corroborating experimental evidence here:
And quantum information is conclusively shown to be transcendent of any material basis here:
The falsification for local realism (reductive materialism) was recently greatly strengthened:
This following video reveals just how downright ‘spooky’ (to use Einstein’s description) quantum entanglement is:
And quantum information is shown to be ‘conserved’ here;
Of related note; I really enjoyed Michael Egnor’s essay on how consciousness is not reducible to matter;
more notes of interest:
Elizabeth Liddle (16.1.2.1.2):
You wrote:
“Well, Sermonti has ignored drift.”
Anything is possible. But here is some biographical background on Sermonti:
“Born in Rome, graduated in agriculture and genetics, he entered the Superior Institute of Health in 1950, founding a department of Microbiological Genetics. He became professor of genetics at the University of Camerino, then at the University of Palermo in 1965, and finally moved to the University of Perugia in 1970, where he is presently emeritus professor and where he manages the Genetics Institute of the University from 1974. From 1970-1971 he presided over the Associazione Genetica Italiana.[1] He is the discoverer of the genetic parasexual recombination in antibiotic-producing Penicillium and Streptomyces. He was vice-president of the XIV International Congress of Genetics held in Moscow and he was appointed as president of the International Committee of the Working Group on Genetics of Industrial Microorganisms.”
It would appear to me that Sermonti’s background in genetics is extensive, and likely more extensive than your own. How probable is it that he has “ignored drift”? Isn’t it more likely that he is well aware of drift, but does not believe that it can accomplish what it is said to accomplish in standard neo-Darwinism? And if someone with this level of expertise in a field which is not your own holds an opinion different from your own, wouldn’t it make more sense for you to inquire into the basis of his judgment than to dismiss his view with a comment that implies that he is either (a) ignorant of the basic facts in his field or (b) unusually careless in his reasoning?
BA77 and Joseph,
You two have a special hypocrisy in your use of evidence.
Designed experiments are out, oh, except when they are done by your side. For example, how many time have you cited Gauger’s Biocomplexity paper? Maybe you should write her, and tell her a directed evolution (however poorly designed) experiment has no bearing on evolution.
Oh, and ‘sequence comparisons’ mean nothing, except say, in the original post, or when Behe uses them to estimate the rate of evolution,for example, in Malarial resistance. He not only uses them, and must presume methodological naturalism. Suppose a designer continually reverted the mutations, meaning the rate of evolution was much greater but washed out by design. Behe has to assume that didn’t happen.
You see the issue. You try to dispense with evolutionary lab experiments and sequence comparison then in the very next breath, cite ID evidence that uses these very methods.
Problem?
Joseph,
“you don’t have any evidence taht gene duplication and recombination are blind, undirected chemical processes”
I don’t know what you mean by this. We can perform several types of recombination in a test tube, with purified components, like any other chemical reaction.
Gene duplication has understood physical mechanisms accounting for it.
Do you not know how these processes work, or are you saying there is a chance a designer is pulling the strings?
DrREC, despite what you may think of my ‘hypocritical’ standard for science, the standard for empirical science is brutally unchanging in its threshold of satisfaction and requires nothing less than a actual empirical DEMONSTRATION for what you are claiming, and in such resolute firmness empirical science is the very antithesis of hypocrisy!!!. You claim that sequence comparisons prove protein evolution from one remote island of functionality to the next remote island of functionality is true for neo-darwinian evolution. Yet, when I point out that you have not actually changed any functional protein to any other functional protein, by Darwinian means (Lenski, Behe, Axe) you claim that you don’t need to demonstrate as such and that sequence comparisons are all fine and well. Well, I’m sorry to hurt your feelings DrREC, but it is not me that requires that this extremely trivial threshold to be met (actually you would have to actually demonstrate Body Plan morphogenesis as well, to satisfy empirical science, but that is digressing), it is empirical science itself that demands you actually demonstrate what you say can be done, by neo-Darwinian means, to actually BE DONE by neo-Darwinian means. And as previously referenced here:
http://www.uncommondescent.com.....ent-399693
There is actual, and ample, DEMONSTRATED empirical evidence that severely questions the legitimacy of your claims!!!
DrREC, gene duplication suffers from the same lack of empirical support as you claim for protein evolution does:
Well, that was some non-answer.
Are experimental evolution approaches valid, or do you want to write a letter to Bio-complexity?
Are sequence comparisons valid, or do you disavow the original post and Behe’s analyses contributing to the edge of evolution, etc.?
You can’t reject the evidence I provided, and accept those.
DrREC, this following evidence is actual empirical evidence from the lab, and the best models we have, not sequence comparison from the imagination of neo-Darwinists as your evidence is:
DrREC:
Nice false accusation.
I never said nor implied such a thing. However your position doesn’t have any experiments that support its grand claims.
“you don’t have any evidence taht gene duplication and recombination are blind, undirected chemical processes”
DrREC:
Computers run via understood physical mechanisms, as do automobiles. And no need for the designers to pull the strings in either case.
PROGRAMMING DrREC- gene duplications are directed by the internal programming of the organism/ cell.
“PROGRAMMING DrREC- gene duplications are directed by the internal programming of the organism/ cell.”
Really?
In a simple cell like E. coli, known to have gene duplications-
1) Where does the ‘internal programming’ to determine what gene to duplicate and the mechanism to do that exist? Which genes are involved?
2) If this is part of the cell’s programming, why isn’t it deterministic? Why doesn’t the whole population execute the program at once? Can you present evidence for such? I’ve never heard of such an observation.
3) How are unused ‘programs’ to emerge later maintained in the face of genetic entropy? Without purifying selection, information is lost.
BA,
You ask for evidence which I provide. You accuse it of just being inference from sequence alignments and designed experiments. I point out the hypocrisy of you citing data using that very same methodology. To refute this point, you list articles that use the same methodology!
Unbelievable.
DrREC, you cite gene duplication in bacteria as ‘proof’ for neo-Darwinism, well let’s see what the real world empirical science says about the gene duplication scenario in bacteria and not what your imagination is saying is happening:
This following paper clearly reveals that there is a ‘cost’ to duplicate genes that further precludes the scenario from being plausible:
This recent paper also found the gene duplication scenario to be highly implausible:
Thus once again the ‘real’ evidence argues forcefully against what you imagine to be possible. Moreover Lenski’s Long Term e-coli shows that even ‘simple’ point mutations interfere with each other, preventing the ‘building’ of functional complexity/information. ,,, Perhaps if you click your heals three times you shall wake up DrREC???
DrREC, it certainly is not ‘the very same’ methodology, since sequence comparisons of proteins of different functions are not a actual demonstration that a functional protein can evolve into another functional protein!!! Exactly how does you just SAYING sequence A evolved into sequence B help you overcome the EXPERIMENTAL evidence that finds severe thermodynamic stability for any given functional protein, plus experimental evidence for extreme rarity for ‘islands of functionality’ of functional proteins, and the obvious observation that this calls into question the very claim you are making??? i.e. You have no experimental support for your position but merely the assertion that it is so!!! This ‘sequence comparison’ of yours is not even close to satisfying the demands of empirical science DrREC!!! Whereas the observation of rarity of functional proteins comes directly from what the empirical science is telling us, not from what we ‘wish’ the rarity, or non-rarity, to be!!!
Moreover, your cited ‘designed’ experiment, which developed several ‘strategies’ for overcoming the many ‘dead ends’ of protein evolution, that they themselves readily acknowledge to be prevalent, is a complete joke for you to use as proof of the ability of proteins to ‘naturally evolve’ as far as empirical science is concerned, for it is precisely those many ‘naturally occurring’ dead ends for protein evolution, that they readily acknowledge and are clearly ‘designing strategies’ to overcome, that is the very question under debate!!! i.e. Can neo-Darwinism, and only neo-Darwinism, traverse the chasms of non-functionality between proteins???
further notes:
Quantum Entanglement falsified the reductive materialistic framework upon which neo-Darwinism happens to be built;
And yet quantum entanglement, which falsified the reductive materialistic framework upon which neo-Darwinism is built, is found to be within molecular biology, on a massive scale, especially including proteins.
Moreover, quantum information is found to be ‘conserved’:
So basically DrREC, for you to cling to neo-Darwinism, in spite of what the empirical science is telling us, you end up being completely detached from how reality is actually constructed;
“PROGRAMMING DrREC- gene duplications are directed by the internal programming of the organism/ cell.”
DrREC:
Yes, the alternative of stuff just happens cannot be tested and therefor is unscientific.
Internal means inside of the organism. cell, just as I stated.
Why would it be deterministic? Why would the whole population execute the same program at once? Haven’t you ever heard of different people searching for a different solution to the same problem? The evidence for programming is in the way the cells transcribe, translate- well just about everything they do.
Again what is the alternative besides “it just does” these things?
Who said they are maintained?
And yet, in the course of ten years, a tiny population of bacteria evolved a new protein function requiring three independent mutations.