Homologies, differences and information jumps

_{Giuseppe Puccio

February 1, 2016

Intelligent Design}

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In recent posts, I have been discussing some important points about the reasonable meaning of homologies and differences in the proteome in the course of natural history. For the following discussion, just to be clear, I will accept a scenario of Common Descent (as explained in many recent posts) in the context of an ID approach. I will also accept the very reasonable concept that neutral or quasi-neutral random variation happens in time, and that negative (purifying) selection is the main principle which limits random variation in functional sequences.

My main points are the following:

Given those premises, homologies through natural history are certainly an indicator of functional constraints, because they mean that some sequence cannot be significantly transformed by random variation. Another way to express this concept is that variation in a functional sequence with strong functional constraints is not neutral, but negative, and therefore negative selection will in mot cases suppress variation and conserve the functional sequence through time. This is a very important point, because it means that strong homologies through time point to high functional complexity, and therefore to design. I have used this kind of argument, for example, for proteins like the beta chain of ATP synthase (highly conserved from LUCA to humans) and Histone H3 (highly conserved in all eukaryotes).
Differences between homologues, instead, can have two completely different meanings:

2a) They can be the result of accumulating neutral variation in parts of the molecule which are not functionally constrained
2b) They can be the expression of differences in function in different species and contexts

I do believe that both 2a and 2b happen and have an important role in shaping the proteome. 2b, in particular, is often underestimated. It is also, in many cases, a very good argument for ID.

Now, I will try to apply this reasoning to one example. I have chosen a regulatory protein, one which is not really well understood, but which has certainly an important role in epigenetic regulation. The protein is called “Prickle”, and we will consider in particular the one known as “Prickle 1”. It has come to my attention trough an interesting paper linked by Dionisio (to whom go my sincere thanks and appreciation):

Planar polarization of Vangl2 in the vertebrate neural plate is controlled by Wnt and Myosin II signaling

In brief, Prickle is a molecule implied, among other things, in planar polarization events and in the regulation of neural system in vertebrates.

Let’s have a look at the protein. From Wikipedia:

Prickle is part of the non-canonical Wnt signaling pathway that establishes planar cell polarity.^[2] A gain or loss of function of Prickle1 causes defects in the convergent extension movements of gastrulation.^[3] In epithelial cells, Prickle2 establishes and maintains cell apical/basal polarity.^[4] Prickle1 plays an important role in the development of the nervous system by regulating the movement of nerve cells.^[5

And:

Mutations in Prickle genes can cause epilepsy in humans by perturbing Prickle function.^[12] One mutation in Prickle1 gene can result in Prickle1-Related Progressive Myoclonus Epilepsy-Ataxia Syndrome.^[2] This mutation disrupts the interaction between prickle-like 1 and REST, which results in the inability to suppress REST.^[2] Gene knockdown of Prickle1 by shRNA or dominant-negative constructs results in decreased axonal and dendritic extension in neurons in the hippocampus.^[5] Prickle1 gene knockdown in neonatal retina causes defects in axon terminals of photoreceptors and in inner and outer segments.^[5]

The human protein is 831 AAs long.

Its structure is interesting: according to Uniprot, in the first part of the molecule we can recognize 4 domains:

1 PET domain: AAs 14 – 122

3 LIM zinc-binding doamins: AAs 124 – 313

In the rest of the sequence (AAs 314 – 831) no known domain is recognized.

Here is the FASTA sequence of the human protein, divided in the two parts (red: 4 domain part; blue: no domain part):

>sp|Q96MT3|PRIC1_HUMAN Prickle-like protein 1 OS=Homo sapiens GN=PRICKLE1 PE=1 SV=2
MPLEMEPKMSKLAFGCQRSSTSDDDSGCALEEYAWVPPGLRPEQIQLYFACLPEEKVPYV
NSPGEKHRIKQLLYQLPPHDNEVRYCQSLSEEEKKELQVFSAQRKKEALGRGTIKLLSRA
VMHAVCEQCGLKINGGEVAVFASRAGPGVCWHPSCFVCFTCNELLVDLIYFYQDGKIHCG
RHHAELLKPRCSACDEIIFADECTEAEGRHWHMKHFCCLECETVLGGQRYIMKDGRPFCC
GCFESLYAEYCETCGEHIGVDHAQMTYDGQHWHATEACFSCAQCKASLLGCPFLPKQGQI
YCSKTCSLGEDVHASDSSDSAFQSARSRDSRRSVRMGKSSRSADQCRQSLLLSPALNYKF
PGLSGNADDTLSRKLDDLSLSRQGTSFASEEFWKGRVEQETPEDPEEWADHEDYMTQLLL
KFGDKSLFQPQPNEMDIRASEHWISDNMVKSKTELKQNNQSLASKKYQSDMYWAQSQDGL
GDSAYGSHPGPASSRRLQELELDHGASGYNHDETQWYEDSLECLSDLKPEQSVRDSMDSL
ALSNITGASVDGENKPRPSLYSLQNFEEMETEDCEKMSNMGTLNSSMLHRSAESLKSLSS
ELCPEKILPEEKPVHLPVLRRSKSQSRPQQVKFSDDVIDNGNYDIEIRQPPMSERTRRRV
YNFEERGSRSHHHRRRRSRKSRSDNALNLVTERKYSPKDRLRLYTPDNYEKFIQNKSARE
IQAYIQNADLYGQYAHATSDYGLQNPGMNRFLGLYGEDDDSWCSSSSSSSDSEEEGYFLG
QPIPQPRPQRFAYYTDDLSSPPSALPTPQFGQRTTKSKKKKGHKGKNCIIS

So, this is a very interesting situation, which is not so rare. We have the first part of the sequence (313 AAs) which configures well known and conserved domains, while “the rest”(517 AAs) is apparently not understood in terms of structure and function.

So, to better understand what all this could mean, I have blasted those two parts of the human molecule separately.

(Those who are not interested in the technical details, can choose here to go on to the conclusions 🙂 )

The first part of the sequence (AAs 1 – 313) shows no homologies in prokaryotes. So, we are apparently in the presence of domains which appear in eukaryotes.

In fungi, we find some significant, but weak, homologues. The best hit is an expect of 2e-21, with 56 identities and 93 positives (99.4 bits).

Multicellular organisms have definitely stronger homologies:

C. elegans: 144 identities, 186 positives, expect 2e-90 (282 bits)

Drosophila melanogaster: 202 identities, 244 positives, expect 5e-152 (447 bits)

Let’s go to non vertebrate chordates:

Cephalochordata (Branchiostoma floridae): 222 identities, 256 positives, expect 6e-165 (484 bits)

Tunicata (Ciona intestinalis): 196 identities, 241 positives, expect 2e-149 (442 bits)

Now, vertebrates:

Cartilaginous fishes (Callorhincus milii): 266 identities, 290 positives, expect 0.0 (588 bits)

Bony fishes (Lepisosteus oculatus): 274 identities, 292 positives, expect 0.0 (598 bits)

Mammals (Mouse): 309 identities, 312 positives, expect 0.0 (664 bits)

IOWs, what we see here is that the 4 domain part of the molecule, absent in prokaryotes, is already partially observable in single celled eukaryotes, and is strongly recognizable in all multicellular beings. It is interesting that homology with the human form is not very different between drosophila and non vertebrate chordates, while there is a significant increase in vertebrates, and practical identity already in mouse. That is a very common pattern, and IMO it can be explained as a mixed result of different functional constraints and neutral evolution in different time splits.

Now, let’s go to “the rest” of the molecule: AAs 314 – 831 (518 AAs). No recognizable domains here.

What is the behaviour of this sequence in natural history?

Again, let’s start again from the human sequence and blast it.

With Prokaryotes: no homologies

With Fungi: no homologies

C. elegans: no homologies

Drosophila melanogaster: no homologies

Let’s go to non vertebrate chordates:

Cephalochordata (Branchiostoma floridae): no significant homologies

Tunicata (Ciona intestinalis): no significant homologies

So, there is no significant homology in the whole range of eukaryotes, excluding vertebrates and including chordates which are not vertebrates.

Now, what happens with vertebrates?

Here are the numbers:

Cartilaginous fishes (Callorhincus milii): 350 identities, 429 positives, expect 0.0 (597 bits)

Bony fishes (Lepisosteus oculatus): 396 identities, 446 positives, expect 0.0 (662 bits)

Mammals (Mouse): 466 identities, 491 positives, expect 0.0 (832 bits)

IOWs, what we see here is that the no domain part of the molecule is practically non existent in prokaryotes, in single celled eukaryotes and in all multicellular beings which are not vertebrates. In vertebrates, the sequence is not only present in practically all vertebrates, but it is also extremely conserved, from sharks to humans. So, we have a steep informational jump from non chordates and non vertebrate chordates, where the sequence is practically absent, to the very first vertebrates, where the sequence is already highly specific.

What does that mean from an ID point of view? It’s simple:

a) The sequence of 517 AAs which represents the major part of the human protein must be reasonably considered highly functional, because it is strongly conserved throughout vertebrate evolution. As we have said in the beginning, the only reasonable explanation for high conservation throughout a span of time which must be more than 400 million years long is the presence of strong functional constraints in the sequence.

b) The sequence and its function, whatever it may be (but it is probably an important regulatory function) is highly specific of vertebrates.

We have here a very good example of a part of a protein which practically appears in vertebrates while it is absent before, and which is reasonably highly functional in vertebrates.

So, to sum up:

Prickle 1 is a functional protein which is found in all eukaryotes.
The human sequence can be divided in two parts, with different properties.
The first part, while undergoing evolutionary changes, is rather well conserved in all eukaryotes. Its function can be better understood, because it is made of known domains with known structure.
The second part does not include any known domain or structure, and is practically absent in all eukaryotes except vertebrates.
In vertebrates, it is highly conserved and almost certainly highly functional. Probably as a regulatory epigenetic sequence.
For its properties, this second part, and its functional sequence, are a very reasonable object for a strong design inference.

I have added a graph to show better what is described in the conclusions, in particular the information jump in vertebrates for the second part of the sequence:

Graph3

Note: Thanks to the careful checking of Alicia Cartelli, I have corrected a couple of minor imprecisions in the data and the graph (see posts #83 and #136). Thank you, Alicia, for your commitment. The sense of the post, however, does not change.

Those who are interested in the evolutionary behaviour of protein Prickle 2 could give a look at my posts #127 and #137.

Comments

Zachriel: OK, it seems that we almost agree on the following ideas: Weak binding to ATP is a function, but it is not a naturally selectable function, and certainly it is not an enzymatic activity. The original protein has low specificity. Engineered evolution increases the specificity. Regarding your last statement: "The folding was probably inefficient, but if they didn’t fold, they wouldn’t bind specifically." just a couple of comments: a) I don't think there is a clear-cut separation between "folding" as we see it in most functional proteins and "some minimal 3D structure" which is probably recognizable in many sequences which essentially do not fold in the strict sense of the word. IOWs, we usually speak of protein folding referring to the very efficient, complex and ordered folding process which transforms a very long linear sequence into a very definite 3D form, with specific functions. So, we could say that most functional proteins which we observe in the natural world have a very specific and ordered folding. Again, that is not a general principle, and there are many functional proteins which do not fold in the traditional sense. So, let's say that the original sequences in the Szostak experiment had probably "some minimal 3D structure", which you call "inefficient folding". That was enough to confer weak ATP binding, and nothing more. In no way we can assume that those sequences presented any folding comparable to that of known functional proteins, while the engineered protein derived from them certainly presented some definite ordered folding. b) I am still not sure of what you mean with "specific". Chemical bindings are often very specific. The binding of Hydrogen to Oxygen to make water is specific and strong. But is is not supported by any folding whatsoever, only chemical properties. So is the binding of Phosphate to ADP to generate ATP. Why do you think that only reactions favored by protein folding are "specific"? Moreover, many highly sophisticated reactions which involve folded proteins are not very specific. For example, the interaction between antibodies and antigens in the primary immune response is typically a low affinity and low specificity reaction, while antibody maturation enhances both affinity and specificity of the molecules.gpuccio_{March 23, 2016
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Dionisio: 3D folding is very important in many proteins, probably not in all. In enzymes, the specific form of the molecules allows stronger binding and specific positioning of the substrates, and helps the enzymatic activity. So, the protein acts as a machine which has a specific form, so that it can receive the substrates, bind them, change their form or biochemical status, and bind them together, or separate them. The cooperation of form and biochemistry is a very powerful tool, and biochemical reactions which would never happen spontaneously, or would happen only very very slowly, are hugely helped and accelerated. In general, it is true that the 3D structure is determined by the primary structure (the sequence of AAs). However, that is not always a fixed relationship. Moreover, the tertiary structure is not a fixed reality, and it is often flexible and constantly changing. Our models of 3D structure are only a reasonable approximation of reality. Computing the 3D structure of a protein from the primary sequence is a very hard task: it is very difficult, and it requires huge computational resources, usually higher than those we can use. However, it is often possible to approximate some structure by reasonable shortcuts, for example by comparing the sequences with others whose structure has been directly analyzed. At present, the best way to determine the 3D structure of a protein is to study it directly, through a biophysics approach. The Protein Data Bank (PDB) is a very good resource for known structures of proteins.gpuccio_{March 23, 2016
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EugeneS: Therefore evolution spans over chemistry as well, and who knows what else. The word "evolution" has many uses, however, the biological Theory of Evolution does not explain stellar evolution or the evolution of the works of Hemingway. Dionisio: Is that a reason why the exact 3D shape of a folded protein is so important for its intended functioning? The three-dimensional shape, including the distribution of charges is the reason why proteins can be very specific to their substrates. If it were simple chemical affinity, then they would bind indiscriminately to many different substrates. Dionisio: Is that 3D shape determined by the sequence of AAs in the polypeptide? That, and the actual process of folding. Many proteins require helpers to fold. Dionisio: IOW, given a sequence of AAs, is there a known algorithm to display the correct 3D shape of the folded protein? Protein folding is a complex process, involving thousands of atoms, and is not easy to simulate algorithmically. It can be done for some proteins, but requires large amounts of computational resources. https://en.wikipedia.org/wiki/Lattice_proteinZachriel_{March 23, 2016
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gpuccio: Now, as I think we have already discussed in the past, a protein which just weakly binds ATP is not an enzyme, because it does not “accelerate, or catalyze” any chemical reaction. But it is a function. gpuccio: Indeed, the engineering can contribute some specific folding which enhances and makes different the original weak binding, so that in the end some chemical reaction of the substrate may be catalyzed. That's exactly what happens. The protein has a three-dimensional structure that conforms to the substrate. The original protein has low specificity. Evolution increases the specificity. gpuccio: I maintain that there is absolutely no evidence that folding ... The folding was probably inefficient, but if they didn't fold, they wouldn't bind specifically.Zachriel_{March 23, 2016
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gpuccio @881
They are parts in a folded protein where chemical binding and other chemical activities are enhanced and helped by the 3D configuration of the whole molecule.
Is that a reason why the exact 3D shape of a folded protein is so important for its intended functioning? Is that 3D shape determined by the sequence of AAs in the polypeptide? IOW, given a sequence of AAs, is there a known algorithm to display the correct 3D shape of the folded protein?Dionisio_{March 23, 2016
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Zachriel, It means you haven't ~~understood the theory of evolution~~ been indoctrinated well enough. It can indeed explain everything. Motion of particles of matter is evolution, chemical reactions are natural selection. After all, there is no difference, allegedly, between life and non-life. Therefore evolution spans over chemistry as well, and who knows what else. The funny thing is all this Plato said ages ago. Darwin did not bring anything new. Nor did any other big fan of evolutionism. These fables appear new only because we all lack classical education.EugeneS_{March 23, 2016
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Zachriel: From Wikipedia: "A chemical bond is a lasting attraction between atoms that enables the formation of chemical compounds. The bond may result from the electrostatic force of attraction between atoms with opposite charges, or through the sharing of electrons as in the covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" such as covalent or ionic bonds and "weak bonds" such as Dipole-dipole interaction, the London dispersion force and hydrogen bonding." From Wikipedia: "Enzymes are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of the process are called substrates and the enzyme converts these into different molecules, called products." Now, as I think we have already discussed in the past, a protein which just weakly binds ATP is not an enzyme, because it does not "accelerate, or catalyze" any chemical reaction. Simply binding a substrate by some chemical bond is not an enzymatic activity. Now, if I remember well, some enzymatic activity (ATPase) was demonstrated in particular circumstances for a very late derivation of the Szostak protein. Certainly, no ATPase activity has ever been demonstrated for the original sequences in the random pool, which were never studied in detail, and certainly it would be very unlikely to assume it existed, given the weak binding of ATP by those sequences. Is it possible that a weak chemical binding may evolve into a stronger bond, and even into some enzymatic activity, by protein engineering? Sure it is. Indeed, the engineering can contribute some specific folding which enhances and makes different the original weak binding, so that in the end some chemical reaction of the substrate may be catalyzed. That's what active sites are. They are parts in a folded protein where chemical binding and other chemical activities are enhanced and helped by the 3D configuration of the whole molecule. So, I maintain that there is absolutely no evidence that folding and enzymatic activity were present in the original random sequences of Szostak's experiment.gpuccio_{March 23, 2016
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gpuccio: Why do you say that a simple chemical bond would not be specific? Perhaps you could explain what chemical bond you have in mind, and how this could evolve into an enzymatic affinity.Zachriel_{March 22, 2016
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Zachriel: Why do you say that a simple chemical bond would not be specific? I don't understand. Any bond is specific to the things that are bound. Could you explain what you mean?gpuccio_{March 22, 2016
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gpuccio: A weak binding of ATP is not an enzymatic activity, just a chemical bond. That is incorrect. If it were a simple chemical bond, it wouldn't be specific, and it couldn't be optimized.Zachriel_{March 22, 2016
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Zachriel: "The biological Theory of Evolution doesn’t explain the behavior of quantum particles, or the explosion of supernovas, among other things." Think about it. If it were really necessary...gpuccio_{March 22, 2016
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Zachriel: A weak binding of ATP is not an enzymatic activity, just a chemical bond.gpuccio_{March 22, 2016
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EugeneS: Tell us what evolution cannot explain. The biological Theory of Evolution doesn't explain the behavior of quantum particles, or the explosion of supernovas, among other things.Zachriel_{March 22, 2016
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Zachriel Tell us what evolution cannot explain. Theories that can explain everything are not scientific.EugeneS_{March 22, 2016
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gpuccio: Binding does not happen only because of folding, at lest not weak binding. An enzyme binds by conforming to the specific shape and charge of the substrate. If it doesn't conform, then it wouldn't be specific, and it couldn't evolve into a tighter fit. gpuccio: You bet! But evolution doesn't care about perfection, but differences, in this case, differences in function. Once you have a selectable function, then evolution can improve the fit. That is also shown by Keefe & Szostak.Zachriel_{March 22, 2016
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Zachriel: "If they didn’t fold, they wouldn’t bind." Why? Binding does not happen only because of folding, at lest not weak binding. And remember, there are functional proteins which do not fold. "What you can reasonably say is that they weren’t in a very precise configuration." You bet! :)gpuccio_{March 22, 2016
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EugeneS: The claim that all complexity in the biosphere can be explained as RV+NS is plain wishful thinking and has no empirical basis. Evolution can explain the origin of a vast number of complex structures in biology. However, understanding the precise history of specific structures is another matter. Appeal to extraneous and unevidenced entities is scientifically vacuous, while hypotheses concerning known mechanisms have been scientifically fruitful.Zachriel_{March 22, 2016
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Me_Think 868 I respect your view.EugeneS_{March 22, 2016
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Zachriel, "None whatsoever". Depends on the claim. The claim that all complexity in the biosphere can be explained as RV+NS is plain wishful thinking and has no empirical basis. What can be empirically demonstrated is radically different from the grand Darwinian claims. As you may remember me saying to you many times, the human ability to walk does not mean we can walk to the Moon.EugeneS_{March 22, 2016
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EugeneS @ 859
You raised an important issue. Which option does one prefer: 1. To continue to make believe we know the answer. 2. To honestly acknowledge fundamental problems in the current understanding of what life is
I will continue to believe that we will find the answer. A year ago majority didn't believe we can detect the incredibly faint gravitational wave, a few years ago detecting Higgs boson was just a figment of LHC scientists imagination. Yet we detected both. Biology just needs more interdisciplinary research to find answers to perplexing problems.Me_Think_{March 21, 2016
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Mung: So gradualism is false. That doesn't necessarily follow, however, from studies of network evolution, we would expect lots of small changes, a few big changes, and the occasional revolution. However, even the revolutions would generally take place over thousands of generations.Zachriel_{March 21, 2016
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Zachriel: The RV part of your equation can be very complex, including everything from point-mutations to recombination to endosymbiosis. So gradualism is false. Glad you finally admit it.Mung_{March 21, 2016
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EugeneS: What Darwinian evolution really claims is that all observed biological complexity with statistically significant levels of functional information can be generated by RV+NS. None whatsoever? You mean generations of scientists have never found any evidence to support their claims? The RV part of your equation can be very complex, including everything from point-mutations to recombination to endosymbiosis. gpuccio: No, the folding was shown only in the final engineered proteins. If they didn't fold, they wouldn't bind. What you can reasonably say is that they weren't in a very precise configuration. gpuccio: I am sure that your theory could explain even a fossil of a chimp dating 4 billion years ago! Um, no.Zachriel_{March 21, 2016
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bill cole: "Io vivo per lei", here, means "I live for her", and I suppose it means "the music". In italian, music is a feminine word. "Lei" can also mean "you" in the formal way of addressing a person. But in the friendly way, which would be used by a lover, it would be "Io vivo per te".gpuccio_{March 21, 2016
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Zachriel: "Of course there is. For instance, common descent implies a historical progression." I am sure that your theory could explain even a fossil of a chimp dating 4 billion years ago! You know, accelerated evolution in reproductive isolation, and some selective extinction: what could be unexpected, when we have such easy tools in our hands? :)gpuccio_{March 21, 2016
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Zachriel: "That means the sequences folded into a three-dimensional structure capable of binding to ATP specifically." No, the folding was shown only in the final engineered proteins. The original sequences were never studied, and there is no evidence at all that they had any significant folding.gpuccio_{March 21, 2016
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Zachriel, "Common descent implies a historical progression" Common descent is assumed not only by Darwinian evolution. What Darwinian evolution really claims is that all observed biological complexity with statistically significant levels of functional information can be generated by RV+NS. This claim was and is without any empirical support.EugeneS_{March 21, 2016
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gpuccio: Again? The data doesn't go away because it doesn't fit your narrative. gpuccio: That is simply not true.
Keefe & Szostak: Starting from a library of 6 * 10^12 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP. This selection yielded four new ATP binding proteins that appear to be unrelated to each other or to anything found in the current databases of biological proteins.
gpuccio: “about 1 in 10^11 random sequences have some weak binding for ATP ..." That means the sequences folded into a three-dimensional structure capable of binding to ATP specifically. gpuccio: There is nothing unexpected in evolutionary theory. Of course there is. For instance, common descent implies a historical progression. EugeneS: The real question is not biological evolution ... Which is why Charles Darwin has been forgotten in the biological sciences.Zachriel_{March 21, 2016
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Me_Think: You raised an important issue. Which option does one prefer: 1. To continue to make believe we know the answer. 2. To honestly acknowledge fundamental problems in the current understanding of what life is. The second option opens up grand challenges which may lead to reconsidering the philosophical foundations of contemporary science. Fine by me. The main thing is to stop lying to ourselves.EugeneS_{March 21, 2016
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Bill Cole # 851, Absolutely! I have been working in the area of combinatorial search and I am keen to know about the developments on the evolution/evolvability front. Since I do a bit of actual hands-on programming myself, people like Zachriel do not impress me with their stale arguments dating back to the times of evolutionist euphoria. The likes of Zachriel always conflate natural selection with intelligent search guidance. All evolution can really achieve is noise compared to the amount of instructions such information-rich systems as organisms need to self-assemble and metabolize. Biological evolution to even kick off needs intelligence. The real question is not biological evolution though but, in David Abel's words, is how the first set of instructions for a living cell came to be. And that is insurmountable for naturalism. OPs like this one easily expose the inability of naturalism to explain biology. That's what I like about them.EugeneS_{March 21, 2016
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