Human evolution: The spin machine in top gear

_{Denyse O'Leary

May 19, 2009

Intelligent Design}

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For a fascinating misreading of what the recently announced Messel Pit fossil really shows, go here:

Scientists have found a 47-million-year-old human ancestor. Discovered in Messel Pit, Germany, the fossil, described as Darwinius masillae, is 20 times older than most fossils that explain human evolution.

That fossil doesn’t “explain” human evolution; it complicates the picture.

The theory that was gaining ground was that humans were descended from tarsier-like creatures, but this fossil, touted as a primate ancestor, is a lemur-like creature.

Often, I hear from people attempting to patch the cracks in the unguided Darwinian evolution theory, as follows: “We have more information than ever!”

Yes, but what if it is – as in this case – the evidence is contradictory?

Evidence for Theory A subtracts from evidence for Theory B. So if A is right, B must be subtracted from the total. If B is right, A must be subtracted from the total.

Surely, that is pretty obvious. But watching the spin machine in high gear is a fascinating exercise anyway.

No wonder fewer and fewer believe Darwinism.

Comments

Joseph, I defer to your expertise on nested hierarchies. Nevertheless, you seem to be out to lunch here [347]:
Even YECs understand that plants act differently than animals. In a YEC scenario plants do not “reproduce after their own Kind”. That only pertains to animals. So while your point about plants is interesting it does NOT do anything to support your case. So what part of all that don’t you understand?
I understand it, it's just wrong.David Kellogg_{June 6, 2009
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Oramus, Nature is not selecting anything. Nature is not preserving, eliminating or building anything. Rather, organisms express and suppress traits according to need in an algorithmic fashion; a big difference IMB. It is important to not confuse the metaphor with the object of interest.Dave Wisker_{June 4, 2009
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Hi Oramus, It seems from your comment below that you miss the point. There are always offspring that live to adulthood and reproduce regardless of any inherited trait. Both offspring with advantageous traits and without both make it to the finish line. I'm afraid it's you that missed my point entirely. It is not that individuals with both make it to the finish line, its the differential proportions of those with the respective traits that make it that is important.If more with the advantageous trait make it, the trait will become more and more common, sometimes even replaving the less advantageous variant. This is simple, observable, and well-recorded population genetics.Dave Wisker_{June 4, 2009
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Mr Oramus, If I understand you correctly, if I trace the life history of all zygotes from conception to death, there is no difference in reproductive success based on their phenotype? The weak and the strong produce, on average, the same number of offspring that themselves live to reproductive age? The runt of the litter does as well as the alpha male?Nakashima_{June 4, 2009
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Dave Wisker, Thanks for your comment. It seems from your comment below that you miss the point. There are always offspring that live to adulthood and reproduce regardless of any inherited trait. Both offspring with advantageous traits and without both make it to the finish line. In your words, traits will become common then not common, common, then not common. Nature is not selecting anything. Nature is not preserving, eliminating or building anything. Rather, organisms express and suppress traits according to need in an algorithmic fashion; a big difference IMB. Organisms exhibit (as described above)genomic plasticity. Yet they cannot build upon mutations as Neo-Darwinism claims in order to break environmental risk thresholds. Adaptability is not evolution. Evolution, defined in its original sense as an unfolding of life, happened and the past and is finished. What biological activity we witness now is basically the running of a maintenance program; peaks and valleys, peaks and valleys, with no new plateaus reached.Oramus_{June 4, 2009
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Hi Oramus, Natural selection is simply differential reproductive success. Consider any heritable trait. A variant of that trait which enables individuals possessing it to have more offspring who live to adulthood than those which possess other variants will become more common in the population. That is not a figment of the imagination. It is a simple, observable, predictable (indeed inevitable) demographic fact.Dave Wisker_{June 4, 2009
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JayM, Dave Wisker, Natural selection is a figment of the imagination. 1. All animals produce healthy and weak offspring at each generation. 2. Healthy and weak offspring all reproduce. 'Strong' genes and 'weak' genes are both required for the stability of the organism. 3. All animal types survive on the basis of cooperation, not competition. Competitive activity within a group scrambles the gene pool in order keep the reproductive ratio stable; never too many strong, never too many weak. It is the consistent reproduction of both healthy AND weak offspring that allows the animal kingdom the possibility of mutual survival. I.E. the rabbit produces several to keep a couple. The snake produces hundreds to keep several. The insect produces thousands to keep hundreds. In essence, it is the weak that are the pillars of life.Oramus_{June 3, 2009
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re #333 Hi Dave, you said: "A basic grounding in coral reef ecology, especially how communities there are structured would at least prevent you from asking the questions, which, when I attempted to help you, are now so distracting." I see that you have another long post so I will read that before responding, but I think somehow we are talking past each other and not engaging. Because the questions I am asking seem eminently sensible to me, no matter what the structure of coral reef communities look like. I cannot get traction, whether because of my inadequate communication skills or my lack of Ph.D. credentials in science (or anything else - I'm an M.S. guy) but if the difference between life and non-life is information, and who doesn't think that is true, then information is the key. Information MUST be explainable in a coherent and rational way or else nothing has been explained. Let me read your next post and I'll get back to you.tgpeeler_{June 3, 2009
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Biped @ 215:
This ["physically inert meaning"] is the concept that I offered to you as an observationally verifiable entailment of the theory of Design – as per your specific request.
(Emphasis in the original.) This beautifully captures what is misguided in your predicted "observation," and what renders it unretrievably gauzy and scientifically useless in its current form: you confuse theoretical conjecture with observation. Simply put, one doesn't observe concepts. Observation consists in counting, measuring, weighing, noting the positions of indicators, recording velocities and locations, noting operationally defined features, developing photographic plates, and on and on, sometimes with the aid of instrumentation. One cannot "observe" conceptually abstract and operationally undefined notions such as "physically inert meaning." Such a notion belongs at the level of theory, which is constructed to both predict and confer meaning upon specific observations. It is because theory is conceptual rather than observational that entailments are required that arise necessarily from one's theory, in turn giving rise to predictions of specific observable phenomena that can be counted, weighed, measured, and so forth, a process above illustrated by BB theory and the CBR. In your case, what you want to say is that your theory of design necessarily gives rise to physically inert meaning (you don't say why this is a necessary entailment - can't the designer design otherwise? - but that is another problem), AND that physically inert meaning gives rise to particular entailments that CAN be observed (counted, weighed, measured, detected, etc.) in particular contexts. Those predicted observations include _____________, which indeed must be observed or your theory is placed at risk of disconfirmation. This is what I have been requesting throughout, and what you have yet to supply. I notice that Abel does no better. At the end of his article he punts: rather than suggesting empirical findings that flow from his theoretical prose he challenges evolutionary biology to support its theory instead. More generally, the complexity of living organisms, including to whatever degree biological phenomena can be an analogized to the human use of symbols, is the phenomena that calls for explanation, and is not itself, alone, evidence for a particular explanatory theory. Simply stating "design entails physically inert meaning" then pointing to "the function of life" and making the bare assertion that it displays "physically inert meaning" (including the further bare assertions that it is an entailment of design AND can only have arisen from design) does nothing more than restate your hypothesis. That is rather like developing a theory of a murder, then citing the fact that the victim is dead in support of your theory. All theories of the crime culminate in a person being dead. Until ID takes the risk of offering a theory that includes "moving parts" - necessary entailments concerning design, the designer, etc., as well as the unique observational consequences of those entailments - it will remain stillborn as well.Diffaxial_{June 3, 2009
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Mr Joseph, Bold type, like all caps, does not make an assertion more true.Nakashima_{June 3, 2009
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David Kellogg, That's what I found in both places, but I hoped that Joseph could back up his interesting claim.Adel DiBagno_{June 3, 2009
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Joseph [344], about plants:
The Bible is the reference- That and all the Creation websites. Really all you have to do is to write to AiG (for example) and they will explain it to you.
From the AiG website:
Once more the evidence of the real world is seen to be consistent with the truth of Genesis; plants reproduce ‘according to their kind’. That is, gingkos have consistently produced gingkos, pines have consistently produced pines, and magnolias have consistently produced magnolias ever since the Creator spoke them into existence to reproduce ‘after their kind’
The reference is to Gen 1:11, which reads "And God said, Let the earth bring forth grass, the herb yielding seed, and the fruit tree yielding fruit after his kind, whose seed is in itself, upon the earth: and it was so."David Kellogg_{June 3, 2009
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joseph, 1- Plants are very different than animals. In what qualitative way that justifies excluding them from a discussion of macroevolution? 2- Plant genetics is much different than animals In what qualitative way that would exclude them from a discussion of macroevolution?Dave Wisker_{June 3, 2009
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Dave Wisker:
I think you need to justify why this discussion of macroevolution has to be restricted to animals.
I did. 1- Plants are very different than animals. 2- Plant genetics is much different than animals Even YECs understand that plants act differently than animals. In a YEC scenario plants do not “reproduce after their own Kind”. That only pertains to animals. So while your point about plants is interesting it does NOT do anything to support your case. So what part of all that don't you understand?Joseph_{June 3, 2009
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Is there any data which demonstrates any amount of mutational accumulation can take a knuckle-walker and from that get an upright biped? No Do we know what gene, gene or DNA sequences are involved in such a transformation? No If we don’t then how can we scientifically test the premise? We can't but we are comfortable in the fact that it happened so therefor it is science.Joseph_{June 3, 2009
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jospeh, I think you need to justify why this discussion of macroevolution has to be restricted to animals.Dave Wisker_{June 3, 2009
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Adel, The Bible is the reference- That and all the Creation websites. Really all you have to do is to write to AiG (for example) and they will explain it to you.Joseph_{June 3, 2009
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Dave Wisker, There isn't any support for an unguided path to the genetic code. There isn't any support for the nucleotides forming and then linking up to get the intial strand that would be translated. And there definitely isn't any data which demonstrates a ribosome can form via unguided processes. But I hope the work continues as those failures should, sooner or later, demonstrate that the attempts are futile. As I said geologists will find a geological explanation for Stonehenge before anyone finds a non-telic explanation for the genetic code. Then you say:
Plants are sophisticated eukaryotic organisms, and to leave them out of any discussion of macroevolution is ridiculous.
To include plants in a discussion about animals is dishonest. To then link what we see in plants to animals is ridiculous.Joseph_{June 3, 2009
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Nakishima, The point is that Art is using an example that no one is debating. IOW Art is being deceptive. Ya see in order to refute an argument one has to address THAT argument. If one instead presents an example that is not being debated then that is just plain dishonesty. Now if the Bible said that "God Created the first populations of single-celled organisms and Commanded them to evolve into the rich diversity we observe today", then Creationists would accept macro-evolution. However as it stands today there isn't any scientific data which supports that premise.Joseph_{June 3, 2009
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Plants are sophisticated eukaryotic organisms, and to leave them out of any discussion of macroevolution is ridiculous.Dave Wisker_{June 3, 2009
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Joseph, The origin of the genetic code is based purely on speculation that it arose via stochastic processes Actually, Joseph, it does have some experimental support (as the second reference specifically mentions), so to call it purely speculation is incorrect.Dave Wisker_{June 3, 2009
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In a YEC scenario plants do not “reproduce after their own Kind”. That only pertains to animals.
Got a reference?Adel DiBagno_{June 3, 2009
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Mr Joseph, Are we having a scientific discussion or a religious discussion? What does a Bible quote mean to macro-evolution? If there was a line in the Qur'an saying "Allah told me macro-volution is true." would that settle things? Or is it now your position that macro-evolution can happen in plants, but not in animals?Nakashima_{June 3, 2009
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Art Hunt, If you want to demonstrate macro-evolution it would be best if you stayed with animals. Even YECs understand that plants act differently than animals. In a YEC scenario plants do not "reproduce after their own Kind". That only pertains to animals. So while your point about plants is interesting it does NOT do anything to support your case.Joseph_{June 3, 2009
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Dave Wisker, The origin of the genetic code is based purely on speculation that it arose via stochastic processes. However there is no way to scientifically test that premise. And yes if scientists do someday reduce the genetic code to matter, energy, chance and necessity then ID would be falsified. However I predict that Stonehenge will be found to be from geological forces before the genetic code is found to be so reducible.Joseph_{June 3, 2009
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Diffaxial, You have serious issues.
“If natural selection is true, we should observe _______. If we fail to observe _______, then natural selection is at risk of disconfirmation.” “If random variation is true, we should observe _______. If we fail to observe _______, then random variation is at risk of disconfirmation.”
To which you respond:
You’ll notice two things about the forgoing: 1) There is no question
Umm it is the SAME format that you and RB have been using foIDists to fill in those blanks. I and everyone else has notioced that YOU have continually FAILED to fill them in. Instead you blather on. As for reproducing your response I posted a link to it. Now are you going to fill in the blanks or continue to prove that your position is baseless and useless? If natural selection is true, we should observe _______. If we fail to observe _______, then natural selection is at risk of disconfirmation.” “If random variation is true, we should observe _______. If we fail to observe _______, then random variation is at risk of disconfirmation." Your original responses were not even predictions of the theory of evolution. THAT is why I called it a pathetic attempt. IOW all you have done is to demonstrate you don't know much of anything about the theory you are trying to defend.Joseph_{June 3, 2009
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Hi tgpeeler, Premise 1: No information can be originated without the systematic, i.e. rules based, use of symbols. That is what I call “language.” This applies to all human languages and all animal languages as well. We typically think of symbols as letters but they can also be sounds, pictures, movements or gestures, clicks, scents, and so on. Consider the genetic code. At its simplest, the code is a physical association between DNA codons, tRNA anticodons, and the amino acids associated with each tRNA. There is growing experimental evidence that this association could have come about purely due to the stereochemical affinities of these entities. The “rules-based use of symbols” in this case would be the stereochemical affinities between the entities, with the entities themselves being the symbols. The only reason we call this a “code” or a “language” is because we recognize an association between the entities. If the hypothesis for the stereochemical origin of the genetic code is correct, then such a code or language (and the information conatined within) did not require intelligence for it to form. Here are just a few papers (and their abstracts) discussing it: : Grafstein D (1983). Stereochemical origins of the genetic code. J Theor. Biol. 105(11): 157-174 Abstract:
The origin of the genetic code may be attributed to a postulated prebiological stereochemistry in which amino acid dimers, the trans -R,R'-diketopiperazines, interacted with prototype codon and anticodon nucleotide sequences. An intricately coupled stereochemistry is formulated which displays a binary logic for amino acid-codon recognition. It is shown that the diketopiperazine ring system can be inserted between any terminal pair of base paired nucleotides in a codon-anticodon structure with exact registration of complementary hydrogen bonding functional groups. This yields a codon-dimer-anticodon structure in which each amino acid residue is projected towards and interacts with a particular sequence of vicinal nucleotides on either codon or anticodon. The projection direction and the sequence of nucleotides encountered is a strongly coupled function of the choice of codon terminal nucleotide and the handedness of the amino acid. The reciprocal chemical nature of the complementary base pairs drives the selection of dimers containing quite dissimilar and chirally opposed amino acids. Application of the stereochemical model to the in vivo system leads to a general correlation for amino acid-codon assignments. The genetic code is restated in terms of the dimers selected. The profound symmetry of the code is elucidated and this proves useful for correlative and predictive purposes.
Hendry LB, ED Bransome, Jr, MS Hutson & LK Campbell (1981). First approximation of a stereochemical rationale for the genetic code based on the topography and physicochemical properties of "cavities" constructed from models of DNA. PNAS 78(12): 7440–7444 Abstract:
To examine the question of whether or not the genetic code has a stereochemical basis, we used artificial constructs of the topography and physicochemical features of unique "cavities" formed by removal of the second codon base in B-DNA. The effects of base changes on the stereochemistry of the cavities are consistent with the pattern of the genetic code. Fits into the cavities of the side chains of the 20 L amino acids involved in protein synthesis can be demonstrated by using conventional physicochemical principles of hydrogen bonding and steric constraints. The specificity of the fits is remarkably consistent with the genetic code. Yarus, M, JG Caporaso & R Knight (2005). Origins of the genetic code: the escaped triplet theory. Annual Review of Biochemistry 74: 179-198. Abstract:
There is very significant evidence that cognate codons and/or anticodons are unexpectedly frequent in RNA-binding sites for seven of eight biological amino acids that have been tested. This suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid–binding sites to become modern codons and anticodons. We explicitly show that this stereochemical basis is consistent with subsequent optimization of the code to minimize the effect of coding mistakes on protein structure. These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself.
Dave Wisker_{June 3, 2009
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tjpeeler asks: p.s. “Without an understanding of the forces” And what “forces” would those be? Are any of them recognized by physics? Because if they aren’t, then another word game is being played and design and purpose are being smuggled in by the back door. A basic grounding in coral reef ecology, especially how communities there are structured would at least prevent you from asking the questions, which, when I attempted to help you, are now so distracting.Dave Wisker_{June 3, 2009
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Hi jerry, I'll get a few answers into the queue before calling it a night. You asked (among other things):
"But is a random set of amino acids a working protein? What percentage of these could be?"
I cannot give you a complete answer. But I can say with confidence that the upper bound of this "percentage" is on the order of one in 10^10 random sequences or so. This number comes from a variety of combinatorial protein chemistry experiments (phage and mRNA display). This sounds pretty rare. But consider that a very, very dilute solution of such sequences, on the order of 1 picomolar, will have each and every possible functionality in it, if these functionalities are roughly this rare. In other words, 1 in 10^10 is pretty darn frequent when it comes to protein sequence space. You also asked:
"So maybe you might want to comment on that and the chances that a random process maybe in some unused part of the genome first forms a DNA sequence that would lead to a working protein and then also form the necessary other elements in the genome so that it eventually gets transcribed and translated. What has to happen. Because ID believes this is rare. So one of the cases you will have to make is that this is not rare."
One of the linked essays discusses exactly this. Basically, the order of appearance is not as you suppose. The first "step" involves the background transcription and junk RNA that is so ubiquitous. This step is, by all accounts, not at all rare. The second step would involve some incorporation of sequence signals that stabilize the RNA and shunt it out of the "junk RNA" degradation pathway. These processes are also not particularly or impossibly rare. Then comes the origination of the protein-coding region. Fig. 7 of Thompson and Parker (reproduced at the end of this essay) illustrates these processes nicely. IMO, none of these steps in isolation pose probablistic problems, nor do they when considered as a package.Arthur Hunt_{June 2, 2009
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Sigh. I never can shut up. So now this distraction when the major point is completely overlooked. It's about the information. Let's get back to that. Somebody, anybody, tell me either that (1) accounting for information is pointless and or unnecessary, and why, OR (2) tell me how any naturalistic account of information (and language) is coherent. Let's try to stay on point. Information/language is the key. As I have argued for ad nauseam. Honestly, unless the darwinists can get this right none of the rest of it matters because if my questions cannot be answered (and they cannot) intelligence, or mind, is the only game in town. p.s. "Without an understanding of the forces" And what "forces" would those be? Are any of them recognized by physics? Because if they aren't, then another word game is being played and design and purpose are being smuggled in by the back door.tgpeeler_{June 2, 2009
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