Tuesday, December 13, 2016

The proteome complexity myth

A reader pointed me to the ThermoFisher Scientific website. ThermoFisher Scientific is a major supply of scientific equipment and supplies. They created their life sciences wesite to help inform their customers and sell more products. The page I'm interested in is: Overview of Post-Translational Modifications (PTMs). It begins with,

Within the last few decades, scientists have discovered that the human proteome is vastly more complex than the human genome. While it is estimated that the human genome comprises between 20,000 and 25,000 genes (1), the total number of proteins in the human proteome is estimated at over 1 million (2). These estimations demonstrate that single genes encode multiple proteins. Genomic recombination, transcription initiation at alternative promoters, differential transcription termination, and alternative splicing of the transcript are mechanisms that generate different mRNA transcripts from a single gene (3).

The increase in complexity from the level of the genome to the proteome is further facilitated by protein post-translational modifications (PTMs). PTMs are chemical modifications that play a key role in functional proteomics, because they regulate activity, localization and interaction with other cellular molecules such as proteins, nucleic acids, lipids, and cofactors.

The article gives a reference for the claim that the human proteome consists of over one million proteins. The reference (#2) is Jensen (2004). That's a review discussing the characterization of post-translational modifications by mass spectrometry. The only information on the number of possible proteins comes from the caption to Figure 1, which is similar to the figure shown above. The caption says,
The human genome is predicted to contain on the order of 30 000 open reading frames, each of which, on average, may produce five or six different mRNA species. Each of these mRNA species are in turn translated into proteins that are processed in various ways, generating on the order of 8–10 different modified forms of each polypeptide chain. Thus, the human genome may potentially produce on the order of (30 000 × 6 × 10) 1.8 million different protein species.
This is not an appropriate scientific reference. You don't support your own speculations by referencing others who make the same data-free speculations.

Let's pause for a moment and do a little fact-checking. It's simply not true that scientists have discovered that the human proteome is "vastly more complex than the human genome" no matter how you want to interpret that phrase. It's certainly not true that this non-fact was discovered after 1996 (past two decades).

Perhaps what the company representatives meant to say was that there are more different proteins than genes. Some of them are produced by alternative splicing. That fact has been known since the early 1980s. However, the great majority of human genes produce one single functional, polypeptide chain. That doesn't count as a recent discovery that the proteome is "vastly more complex."

This figure shows 100,000 "transcripts" from 25,000 genes implying there are 100,000 different polypeptide chains. There's no evidence to support such a claim and plenty of evidence against it.

It's true that the polypeptide chains produced by translation can be subsequently modified in several ways. That's also a fact that's been known for a lot longer than 1996. Read the textbooks from the 1980s to see descriptions of phosphorylation, glucosylation, and a host of other post-translational modification. Some of these (e.g. phosphorylation) are involved in regulating enzyme activity so there will always be two different versions of the protein (phosphorylated and nonphosphorylated) in the cell. That still doesn't count as "vastly more complex."

In the case of glycosylation, there will be multiple forms, from nascent unglycosylated polypeptide through half a dozen intermediates to the final glycosylated version. That's quite a few but not "vast." Besides, most of those intermediates are transient.

Now, if you combine glycolyated and phosphorylated you can double the number of variants but that's very misleading. What we're really interested in are the total number of functional proteins in a cell and not the number of transient intermediates that might occur during post-translational modification.

Almost all human polypetides are modified by removing the N-terminal methionine residue so I suppose you could honestly say that every gene produces at least two different proteins; one with an initial methionine and one without. Technically, that makes 40,000 different proteins produced by 20,000 protein-coding genes. I don't think that's what people mean when they talk about a complex proteome. What they mean is one million proteins doing different things inside the cell. It's an attempt to explain how humans can be so complex with only (gasp!) 20,000 protein-coding genes.

There are several hundred (~300) different types of post-translational modification known. Some have been discovered recently but many have been known for a long time. I don't know how many different polypeptides (the primary product of translation) are post-translationally modified beyond removing the N-terminal methionine. I suspect it may not be a majority.

Furthermore, I don't know how many post-translational modifications actually contribute to function and how many are just due to "noise." A recent study shows that about 25% of yeast proteins are phosphorylated but less than 10% of phosphrylation sites are well conserved (Studer et al., 2016). The authors conclude that rapidly evolving phosphorylation sites "can contribute strongly to phenotypic diversity."

The authors of the accompanying Insights article have a slightly different take on the results (Matalon et al., 2016). They say,
Such a lack of conservation appears to contradict the textbook view that phosphorylation is strictly controlled and regulates important functions. Whereas certain phosphorylation events do surely regulate function, many may not. Edwin Krebs himself, who received the 1992 Nobel Prize with Edmond Fischer for the characterization of "reversible protein phosphorylation," noted that there likely exists a degree of phosphorylation noise.

Noise—phosphorylation events not selected to carry out a specific function—can provide a simple explanation for the weak evolutionary conservation of phosphosites. Mechanistically, the low degree of sequence specificity required for phosphorylation implies that new kinase recognition motifs can frequently emerge by chance, without having been selected for, and hence need not be conserved. Kinase promiscuity means that even noncanonical substrates may be phosphorylated occasionally, so that abundant proteins can yield subpopulations detectable with mass spectrometry.
I agree with Matalon et al. that noise is probably the explanation for many post-translational modifications.1 This doesn't diminish the claim that the proteome is diverse but it challenges the unstated assumption that proteome complexity is deeply meaningful.

When I refer to the "myth" of proteome complexity, I'm not challenging the idea that there are many more protein variants than there are genes. We could quibble about the exact number but it's almost certainly not true that there are, on average, 40 different functional proteins produced by only 25,000 protein-coding genes. That's what would have to be true if there were one million different proteins in the proteome.

I challenge the people who make this claim to show me the 40 different variants of each of the glycolytic enzymes and the enzymes of the citric acid cycle. Or the 40 different variants for each of the subunits of RNA polymerase or complexes I, II, III, and IV in the mitochondrial membrane.


1. Note the use of conservation as a proxy for function.

Jensen, O.N. (2004) Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Current opinion in chemical biology, 8:33-41. [doi: 10.1016/j.cbpa.2003.12.009]

Matalon, O., Dubreuil, B., and Levy, E.D. (2016) Young phosphorylation is functionally silent. Science, 354:176-177. [doi: 10.1126/science.aai8833]

Studer, R.A., Rodriguez-Mias, R.A., Haas, K.M., Hsu, J.I., Viéitez, C., Solé, C., Swaney, D.L., Stanford, L.B., Liachko, I., and Böttcher, R. (2016) Evolution of protein phosphorylation across 18 fungal species. Science, 354:229-232. [doi: 10.1126/science.aaf2144]

142 comments :

  1. When ThermoFisher starts offering antibodies raised against proteins translated from alternate splices that specifically light up proteins from alternate splicing in cell lysates, then we can start taking them seriously. The webpage you link seems to be primarly focused on post-translational modifications, so it would appear that the alternate splicing part of the page is little more than window dressing for a sales pitch.

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    1. Eric,

      Your comment is spot on. In fact, a potentially useful approach to providing evidence for functional splice variants is to see if they are regularly translated.

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  3. "One gene can encode more than one protein (even up to 1,000). The human genome contains about 21,000 protein-encoding genes, but the total number of proteins in human cells is estimated to be between 250,000 to one million."
    https://proteomics.cancer.gov/whatisproteomics

    If the object of the game is to diminish complexity so that DNA replication errors and natural selection look like creative agents, you're wasting your time. That said, when you've arrived at a suitable excuse, you can move on the to the microbiome.

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    1. OK, txpiper, as Larry said: "I challenge the people who make this claim to show me the 40 different variants of each of the glycolytic enzymes and the enzymes of the citric acid cycle. Or the 40 different variants for each of the subunits of RNA polymerase or complexes I, II, III, and IV in the mitochondrial membrane."

      You're up, buddy, time to back up your talk with evidence!

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    2. txpiper,

      Rather than reading that number and take it for granted, you should have asked how they estimated that number of proteins per tissue. Then you check if that makes sense and if that naturally goes towards that estimate being unchallengeable or not.

      Either way, I don't see how such number would make your imaginary friends real. For your imaginary friends to be real, it's not enough to say "haha, evolution doesn't work with single-point mutations if there's thousands of variants! Muahahahahaha!" The most that would mean is that we might be missing some way in which functions arise, rather than a problem with natural phenomena doing what we see.

      Now, you'll say "aha! you have a bias against "God" muahahahahahaha!!!!!" Well, not against "God," but against considering imaginary beings. "Aha! You evolutionist! You're angry with "God"!!!! Muahahahahahaha!" Well, no. the proper question is whether the bias against considering imaginary beings is justified. Well, yes, the problem is that they're imaginary. So, if you want thinking people to consider imaginary beings as answers to open questions, then you need something better than an open question, you need evidence that those imaginary beings are something other than imaginary beings. In the meantime, I have no option but look for information about nature that might be missing in our scheme of understanding.

      Do you understand this at all?

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    3. photosynthesis,

      Yes, I understand. I didn't provide the link to dispute the number of human proteins and variants. My comment is about the general resistance to, and disappointment in, discoveries that illustrate complexity. (Here's another one: https://www.sciencedaily.com/releases/2016/12/161206111621.htm ) The reason for it is pretty obvious; the more complicated and intricate something is, the less likely it was assembled by chance. The same principle applies to the junk DNA dispute. Materialism is insulted and offended by complexity.

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    4. No, txpiper. Complexity does not indicate that evolution is impossible. Nor does it somehow insult or offend materialism. It does cause us to be totally amazed and awestruck by what the simple processes of mutation, genetic drift, and differential reproduction accomplish.

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    5. txpiper,

      "the more complicated and intricate something is, the less likely it was assembled by chance."

      But we already know that things didn't come by chance. If we thought it was chance we would not be looking for phenomena, such as natural selection (which is not a single phenomenon, but more of a consequence of several factors), or gene duplications, or other things that don't happen strictly at random, but because of, for example, the presence of many repetitive sequences and such.

      "The same principle applies to the junk DNA dispute. Materialism is insulted and offended by complexity."

      I doubt it. The junk DNA dispute also occurs among scientists who don't believe in magical beings. I, for one, first rejected the idea of loads of junk DNA because it seemed to contradicted my understanding of evolution (too focused on natural selection alone). Only after lots of reading and understanding did I accept the idea. Nothing to do with materialism.

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    6. Materialism is insulted and offended by complexity.

      Thus we know that the really complex parts of the course of the Mississippi were designed, and the simple, straight parts are natural - right?

      Heh, heh.

      Gosh, tx, took all of about 5 seconds to think of a real world example that violates your none too well conceived "principle." Wanna try again?

      Oh, and would you please respond to Larry's challenge? (Second request. Expecting crickets, just like the first time.)

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  4. txpiper,

    We are resistant to claims that are not backed by evidence. That's all there is to it.

    If there really were millions of different proteins it wouldn't change the evidence for evolution. Complexity doesn't refute evolution. We still have those nested hierarchies that creationists still can't explain, those same nested hierarchies that evolution explains so well.

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    1. Transportation implements like cars and bikes have nested hierarchies yet they are all output of Intelligent Design. What do you mean "creationists still can't explain"?

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    2. Cars and bikes do not fall into a nested hierarchies. One of the hallmarks of intelligent design is the lack of nested hierarchies.

      For example, you can find the same tire on a Ford and a Chevy, but two different tires on two cars from the same model of Ford. There are tons of examples where a nested hierarchy is violated. We don't see this in life.

      Creationists can't explain why separately created groups of species would fall into a nested hierarchy. For example, they can't explain why there are no species with feathers and three middle ear bones. They can't explain why all species who have hair also have mammary glands. They can't explain why genes that have nothing to do with body morphology also produce the same nested hierarchies that morphology does. As a counterexample, humans move exact copies of genes between species all of the time and easily violate a nested hierarchy.

      This is the evidence that supports evolution, and it doesn't go away if there is a complex system of alternate protein translation.

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    3. Here is one definition: "Groups of related organisms share suites of similar characteristics and the number of shared traits increases with relatedness". I don't see anything categorical here saying that you can't have traits shared by more remote relatives.

      And what does "same tire on a Ford and Chevy" mean? What if you're grouping incorrectly by brand when you should group by vehicle type? If so, indeed you will not see a subcompact tire on a truck or a bus.

      And (if true) what if evolution is the mechanism of creation as opposed to a factory line assembly model or something else you might imagine? People did know for ever that mating perpetuates the species and didn't see a conflict with their religious beliefs.

      Can you explain "why there are no species with feathers and three middle ear bones"? Please don't say "it's an accident of evolution". That's not an explanation.

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    4. danbaur,

      What you are missing is that shared derived characteristics fall into a tree-like pattern. If a mammal and a fish share a feature, then that feature should also be shared by reptiles since reptiles also descended from the same common ancestor.

      This tree-like pattern of shared features does not exist for cars, bikes, buildings, artwork, or any other intelligent design. In fact, when humans design organisms they regularly violate a nested hierarchy. There are mice that have exact copies of jellyfish genes that no other mammal has. There are bacteria with human insulin genes. There are mice with exact copies of human genes that no other ape species has. Time and again we see intelligent designers violating a nested hierarchy, yet no such violations are seen in complex eukaryotes.

      As to why there are no species with feathers and three middle ear bones, the answer is quite simple. None of the ancestors of feathered birds had three middle ear bones. That feature evolved in the mammal branch. That is why you don't see birds with three middle ear bones. An intelligent designer, on the other hand, would be free to mix these adaptations. This is why a nested hierarchy is evidence for evolution and evidence against intelligent design. This evidence does not go away if there are many different translated proteins created from a single gene.

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    5. Danbaur, have you seen those maybe '60's vehicles that look like cars from the front but turn out to have the open cargo spaces of pick-up trucks? They violate any hierarchical categorization of vehicles.

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    6. Eric wrote:

      "Creationists can't explain why separately created groups of species would fall into a nested hierarchy."

      I had a debate with evolutionary biologist Marcus Williams. His main argument to justifiy the tree of life, and common ancestry, was nested hierarchies.

      Nested hiearchy is evidence of pre-programmed adaptation.
      Therefor, it can be explained also by design.

      A designer would use the same toolbox to create distant animals with the same habilities. Like bats and dolphins using echolocation. Presumably, the random road of genetic evolution would not tend to travel the same way twice, particularly to produce complex traits in animals of different lineages.

      Let me quote from several science papers:

      - Orphan genes: An important category of "rogue" genetic data that utterly defies evolutionary predictions is the common occurrence of taxonomically restricted genes, otherwise known as "orphan genes." These are now being discovered in the sequencing of all genomes.
      "Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species."

      - Hundreds of other genes that are common in cephalopods, but unknown in other animals, were found.
      - Octopus : The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.

      - Rofifiers: Of the 28,922 sequences for which they could obtain a match in a public database of other creature's DNA and protein sequences, a significant proportion (more than in any other creature sequenced) did not fit evolutionary expectations of common descent.

      -Phages: We show here that no single gene is found in all phage that can be used as the basis for a classification system.

      "Each new prokaryotic genome that appears contains dozens, if not hundreds, of genes not found in the genomes of its nearest sequenced relatives but found elsewhere among Bacteria or Archaea."
      W. Ford Doolittle Science 286, 1999.

      As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities
      "This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles.

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    7. Ontangelo,

      "A designer would use the same toolbox to create distant animals with the same habilities. Like bats and dolphins using echolocation."

      That's just it. They aren't made using the same toolbox. When you compare the DNA sequence of the Prestin gene amongst dolphins and bats you get the expected species tree. Bat Prestin DNA is more like that of other bats than like that of dolphins. What you are probably referencing is the fact that the amino acid sequence of the proteins are more similar. This kind of ruins your whole argument because a designer wouldn't use a different DNA sequence to produce the same protein sequence, and yet that is exactly what we see with the Prestin gene in echolocating dolphins and bats.

      "Presumably, the random road of genetic evolution would not tend to travel the same way twice, particularly to produce complex traits in animals of different lineages. "

      Your presumptions would be wrong. If there are limited number of roads to travel, then it isn't surprising when the same road is taken. What we wouldn't expect to see is the same exact DNA sequences, and we don't.

      "- Orphan genes: An important category of "rogue" genetic data that utterly defies evolutionary predictions is the common occurrence of taxonomically restricted genes, otherwise known as "orphan genes." These are now being discovered in the sequencing of all genomes.
      "Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species."

      New genes that are restricted to taxons is exactly what we would expect to see with evolution. Do you even understand what you are arguing against?

      ""Each new prokaryotic genome that appears contains dozens, if not hundreds, of genes not found in the genomes of its nearest sequenced relatives but found elsewhere among Bacteria or Archaea."
      W. Ford Doolittle Science 286, 1999."

      I was also careful to explain that I am talking about complex eukaryotes. Lateral genetic transfer is a well known feature of prokaryotic genetics.

      "As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities
      "This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles."

      Dr. Collins is right. It is the PATTERN of similarity that evidences evolution, and that pattern is a nested hierarchy. Haven't you been reading my posts?

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    8. Good discussion, Eric, bwilson, and Otangelo!

      Eric, I hear the tree of life is obsolete now and the replacement still has too many problems.

      Based on the definition I gave and you did not dispute, it's impossible to violate nested hierarchy.

      "An intelligent designer, on the other hand, would be free to mix these adaptations" - yes, but not FORCED by you or anyone else. If you had found the "middle ear bones" in feathered, you would have said "convergent evolution did it". So either way you win? I want that.

      bwilson - doesn't the platypus and others violate any categorization? Isn't categorization artificial by definition?

      Guys, arguing against ID is an impossible task. You're trying to second-guess what someone much smarter than you would do (or even worse: should do or not do). Only in cartoons does a Garfield dominate a Jon.

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    9. "Eric, I hear the tree of life is obsolete now and the replacement still has too many problems."

      It isn't obsolete. The only problem is creationists misrepresenting the science.

      "Based on the definition I gave and you did not dispute, it's impossible to violate nested hierarchy. "

      What is impossible about a species having feathers and three middle ear bones? That would violate a nested hierarchy, and I see no reason why an intelligent designer could not produce such a species.

      "If you had found the "middle ear bones" in feathered, you would have said "convergent evolution did it". So either way you win?"

      I'm sorry, but putting words in my mouth does not an argument make.

      "bwilson - doesn't the platypus and others violate any categorization? Isn't categorization artificial by definition? "

      The platypus is a perfect intermediate and fits nicely in the nested hierarchy. It has fur and mammary glands like more derived mammals. It also lays eggs through a cloaca like our reptilian ancestors.

      "Guys, arguing against ID is an impossible task. You're trying to second-guess what someone much smarter than you would do (or even worse: should do or not do). Only in cartoons does a Garfield dominate a Jon."

      Would an intelligent designer go through all the extra effort just to make life look like it evolved?

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    10. "There is emerging evidence of HGT occurring within the prokaryotes at the single and multicell level and the view is now emerging that the tree of life gives an incomplete picture of life's evolution. It was a useful tool in understanding the basic processes of evolution but cannot explain the full complexity of the situation".

      You read incorrectly: based on definition, one cannot violated nested hierarchy. Period.

      I am not putting words in your mouth. When you find similar features on remotely related branches do you or don't you say "convergent evolution did it"? If yes, that's trying to have it both ways.

      Anyway, the tree is a human construct made to fit a certain view. I don't see how those "cars that look like trucks" are to transportation any different than a platypus is to mammals and reptiles.

      "Would an intelligent designer go through all the extra effort just to make life look like it evolved?" - this is a very silly question. What "extra effort"? Evolution could be 'The Mechanism' of creation. How would you do things differently?

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    11. danbaur,

      You're reading too much into that text. Actually, it is possible to "violate" nested hierarchies. This is how, for example, people figured out that horizontal gene transfer was too extensive in some bacteria. The genes of a single organisms did not comply with a single nested hierarchy, which means that some proportion of genes "violated" nested hierarchy number 1, others "violated" nested hierarchy number 2.

      "When you find similar features on remotely related branches do you or don't you say "convergent evolution did it"? If yes, that's trying to have it both ways."

      I don't know about Eric, but in the bacterial example above, scientists didn't say "convergent evolution" (I suspect creationists said "god-did-it," though). They said, this looks like HGT can be much more extensive than previously thought.

      For convergent evolution to work there's need for evidence. I suspect that you are thinking of similarities in too wide terms, then you charge without thinking much further. But I rather not try and guess.

      "Anyway, the tree is a human construct made to fit a certain view."

      Actually, any conceptualization is a human construct made to see if things fit different views. But tests are involved. If a different model fits better, then the new model overcomes the old one, as long as there evidence for the newer model, etc.

      "What "extra effort"? Evolution could be 'The Mechanism' of creation. How would you do things differently?"

      But then why propose a designer at all if what we see is evolution?

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    12. photosynthesis,

      So if HGT "violates" nested hierarchies and the sky doesn't fall, then nested hierarchies has no merit as argument against creation. Would you tell that to Eric?

      "convergent evolution" has been used as argument for flying insects, birds, and bats. Do you think HGT "did it" for the bats now? What am I charging, and what is your point anyway?

      The model should fit reality, not the other way around. "I have a model that shows..." is never a solid argument (Eric's).

      You do see the evolution of the transportation implements. Do you think that happened without designers? When was the last time you saw something that looked designed and you positively know it was not designed?

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    13. Danbaur, Be careful of arguments regarding convergent evolution. It's easy to argue sloppily using this concept.

      Flying insects, birds, and bats all have wings and fly. To that extent, they are convergent. However, the structure of insect wings, bird wings, and bat wings are very different, as a result of their evolutionary history. The convergence is, obviously, superficial.

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    14. Danbaur, the distinction that horizontal gene transfer is a big thing in bacteria but a very small thing in eukaryotes may seem arbitrary if you don't know much about the biology involved, but it's a legitimate distinction.

      Bacteria and allies can absorb DNA or RNA from their environment directly into the cell where their own DNA resides. Usually they break down the absorbed DNA as food, but it may function as a gene or even be added to the bacterium's own DNA and passed down to all future generations.

      Eukaryotes (organisms with complex cells) don't have the same mechanisms for absorbing DNA whole and keeping it functional. In multicellular organisms, most cells aren't reproductive, so even if they're infected by some transferred DNA, they won't pass it on to the next generation. HGT happens in multicellular organisms, but not often.

      Phylogenetic trees of bacteria are a mess because of HGT. Phylogenetic trees of multicellular eukaryotes (and of single-celled ones as far as I can know) are generally consistent and give reasonable answers. HGT can be found occasionally, and more often gene transfer among closely related species that hybridized, but over all the trees work.

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    15. danbaur,

      "You read incorrectly: based on definition, one cannot violated nested hierarchy. Period."

      I have already given you examples of combinations of shared features that would violate a nested hierarchy, such as a species with three middle ear bones and feathers.

      "I am not putting words in your mouth. When you find similar features on remotely related branches do you or don't you say "convergent evolution did it"? If yes, that's trying to have it both ways."

      First, we are talking about homologous features. Second, you can't point to a single homologous feature that clearly violates a nested hierarchy where I have excused the violation with a plea of convergent evolution. You can't find an example because I have never done so. I don't have it both ways.

      "Anyway, the tree is a human construct made to fit a certain view. I don't see how those "cars that look like trucks" are to transportation any different than a platypus is to mammals and reptiles."

      Nested hierarchies are objective facts, not an illusion of human construction. There are statistical tests that can objectively and empirically detect tree structures. You can read more here:

      http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy

      "this is a very silly question. What "extra effort"? Evolution could be 'The Mechanism' of creation. How would you do things differently?"

      Why even invoke an intelligent designer when all you need is the natural process of evolution?

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    16. danbaur,

      "So if HGT "violates" nested hierarchies and the sky doesn't fall, then nested hierarchies has no merit as argument against creation."

      HGT only rarely occurs in eukaryotes like us. Creationism would not produce a nested hierarchy. Evolution in the absence of HGT would. What do we see in eukaryotes? A nested hierarchy. This indicates that eukaryotes evolved from a common ancestor. That includes everything from mushrooms, to plants, to fish, and to humans.

      ""convergent evolution" has been used as argument for flying insects, birds, and bats. Do you think HGT "did it" for the bats now? What am I charging, and what is your point anyway?"

      The wings of birds, bats, and insects are not homologous features.

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    17. Guys, we're collectively going off the rails with these back and forths.

      Eric, you keep insisting "Creationism would not produce a nested hierarchy". I don't see a valid argument, but will stop here rather that repeat my replies.

      "Nested hierarchies are objective facts" - I see them as models subject to change. Once again, we can agree to disagree.

      photosynthesis "what we see is evolution" and Eric "all you need is the natural process of evolution" - I don't think we even see evolution. We only see related organisms and adaptations which I see as built in and you see as evolution.

      Either way and once again, transportation implements are also related, yet designed. If it looks designed, it is designed unless you have proof to the contrary. You do agree that life looks designed, right?

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    18. Danbaur. First, Creationism could produce absolutely anything. If there is an omnipotent God, it could produce a world full of life that looks like it evolved. You're right.

      There are two problems with this as a hypothesis. First, if the hypothesis can't predict any results, it can't be tested. (It can't be part of science.)

      Second, if God created the world to look evolved (which it does), this means the God lies. God lies about big stuff. If I believed in God, I'd like to think better of him.

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    19. danbaur,

      "So if HGT "violates" nested hierarchies and the sky doesn't fall, then nested hierarchies has no merit as argument against creation."

      I didn't think you'd be the stupid kind (sorry, you left me no option about what to conclude). Nested hierarchies are not "arguments against creation." They're just groupings that occur due to some kinds of divergences. "Creation" is just some fantasy. There's no need for arguments against that crap. Rather, the superstitious people who believe in "creation," need evidence for "creators" if they want others to believe as they do.

      "Would you tell that to Eric?"

      I think he realized that you're an idiot already.

      "convergent evolution" has been used as argument for flying insects, birds, and bats. Do you think HGT "did it" for the bats now? What am I charging, and what is your point anyway?"

      Wow. There I was, trying to give you the benefit of the doubt. Yet, here you are, playing stupidly with "similarities," just as I was about to describe.

      Those are clearly convergent evolution you idiot. So clearly that we don't need a lot of details to notice. You must be an authentic idiot if you think that merely calling something a "wing" should have made us make the mistake of putting together flies, birds, and bats. (Oh! the biblical idiots did that, didn't they? They mistook bats for birds. Their imaginary friend must be that stupid to inspire them to write something so evidently wrong).

      Let me help you make an idiot out of yourself a bit further. HGT would not explain the wings in bats because they're clearly derivative from hands. We can check the bone structure and the way the bat wing develops in the embryo. HGT is horizontal gene transfer you idiot. For that to explain bat wings, the wings would have to be structurally identical to those of whatever you think gave the bats wings by HGT, then the development would have to be the same as in those other life forms, and the genes responsible should be also the same as those in those other life forms, and not similar to genes in close relatives to bats. You'd also need a mechanism for HGT that worked for multicellular organisms. But we don't need to go there, because everything, from the structure to the development to the genes points to bat wings being derived from mammalian hands. Not from bird wings. Not from insect wings.

      Man if you don't see the difference between insect wings, bird wings and bat wings, you must be authentically stupid. But no-kidding-authentically stupid.

      Delete
    20. Danbaur, Second, design is not the default, the null hypothesis. Natural processes are the null hypothesis. If there were good evidence for design, we'd have to take the idea seriously, of course, but there isn't.

      Also, how do you know if something "looks designed"? You know human products are designed because you've seen the design process. Have you seen a design process that could make trees or humans? You have not. Do you even know components that could be parts of that kind of design? No, you don't.

      Take a close look at organisms, too. Are they designed? Think about that platypus you mentioned, nutritious secretions oozing out of its sweat glands; the babies lap this off its chest. Would you design feeding babies that way? I doubt it. Consider your back, with the supports nearly parallel to the spine, virtually guaranteeing back pain. Is this easier to explain by design or by a messy evolutionary process? Is it really design?

      Are there natural processes that could produce organisms? Yes, there are. We don't know all the steps between the biochemistry present on the early earth and the organisms here now, but (1) we do understand some about how biochemistry could become cells and we slowly learn more and (2) the pattern of evolutionary history revealed in fossils is pretty clear, even though we don't know all the pieces.

      Delete
    21. bwilson295, ID is not a hypothesis but a belief (i.e. the ultimate hypothesis). To hold your world together you have certain beliefs too if you like to admit or not. Evolution is one of them that look very flimsy to me. Atheism is the other, right?

      "if God created the world to look evolved (which it does), this means the God lies" - here you're not making sense. The world looks as it does - no one promised you a different look.

      photosynthesis, you looked like a decent person, why do you have to devolve into hooliganism? Or are you just trying to prove "devolution"? Your rant doesn't follow anything I argued so it's not even clear what you're fighting. Maybe you should slow down with the alcohol, meth or whatever you're on.

      Delete
    22. danbaur,

      Why did you have to play the role of an authentic idiot? You jumped over those words like a misinformed idiot and nothing else. What did you expect? Next time try and understand what's going on. Don't talk out of your ass. Don't stupidly mistake insect wings with bird wings with bat wings. Think instead. Unless, of course, you're really that stupid. Then there's nothing you can do about it.

      Delete
    23. photosynthesis,

      The wing quote was from https://en.wikipedia.org/wiki/Convergent_evolution and was used to just illustrate something else that you missed big time. Maybe your argument is with Wikipedia, but not with me. I am not sure you understand what's going on. And hooliganism doesn't help you win any argument.

      Delete
    24. @ danbaur:

      Eric, you keep insisting "Creationism would not produce a nested hierarchy". I don't see a valid argument, but will stop here rather that repeat my replies.

      You're repeating a common creationist trope here: That the nested hierarchy demonstrating common descent is just a human artifact that could be imposed on any set of entities that were "designed." Well, then, why don't any of you actually demonstrate this? e.g. Why not produce a tree of descent using all currently manufactured motor vehicles? To me, this would seem an impossible task. For instance, how is it that cars from Nissan, Ford, Honda, BMW, Mazda, Toyota, Subaru, Mitsubishi, Fiat, and many others all contain airbags made by Takata? Did they all descend from a common ancestor that contained Takata airbags? Problem with that is all of those manufacturers were making cars long before air bags even existed. So how could that be? And you have to go thru that same process with every single component: Every nut, every bolt, every gasket, spark plug, tire, knob, etc.

      I don't see how it can be done but, hey, I'm not a creationist. It's not my claim. So why not put your money where your mouth is, danbaur, and produce an automotive "tree of life." Or, STFU with your empty arguments. Either will do.

      Delete
    25. lutesuite,

      I am not sure what you find so unbelievable. You don't think transportation taxonomic groups fits neatly and completely inside other taxonomic groups ("Nested hierarchy")?

      Grouping by brand is misleading as you don't have brands in organisms. But all vehicles in the same class (say midsize) have similar characteristics that are somewhat different from other classes (tires in the example chosen by someone else above). Takata is not a thing, but airbag is a common characteristic for automobiles but not for bikes.

      What would "a tree of descent using all currently manufactured motor vehicles" show? Just google "evolution of automobile design" and will see some tree sketches.

      Delete
    26. @dandaur you are very much mistaken. Any object can be subjectively grouped into a nested hierarchy, but because it is subjective, all trees drawn would be equally valid and therefore useless. Objective nested hierarchies can only be drawn for objects that reproduce and change, this has been proven mathematically using Markov Chains. Phylogenetic trees are objectively drawn and are statistically significant.

      Delete
    27. bwilson295, ID is not a hypothesis but a belief (i.e. the ultimate hypothesis). To hold your world together you have certain beliefs too if you like to admit or not. . . . Atheism is the other, right?

      I believe, truly believe, that the world is as it appears to be (though we humans individually would miss some of the subtleties). I believe that we can know about about it and that it is worth understanding. I believe that our human reasoning can allow us to understand it, or at least much of it (though we have to work collectively at this because no one of us can know enough).

      As a result of that basic belief, I conclude that we can find a pattern that ties together the observed biodiversity, fossils, geologic processes, astronomy, biochemistry, etc. This pattern involves change in biochemicals and in living organisms, and stretches over billions of years. That pattern is the process we call evolution.

      So for me, evolution is a consequence of evidence plus my basic beliefs.

      Delete
    28. danbaur,

      When I suggest to stop talking out of your ass, and then think before commenting, I was really meaning that you should stop talking out of your ass and think before commenting.

      This piece of shit didn't come from wikipedia, it came right out of your ignorant ass:

      ""convergent evolution" has been used as argument for flying insects, birds, and bats. Do you think HGT "did it" for the bats now? What am I charging, and what is your point anyway?"

      See that idiot? That's the idiocy that you posted, and the idiocy that made me realize how astoundingly stupid you are. You didn't bother to understand my comment. You just took some of my words to produce that monstrosity of astounding stupidity. Mistaking the wings of flies, bats and birds! Pretending that convergent evolution for those is but an excuse! You must think that those wings are identical. "Suggesting" that instead we should explain those wings as HGT! You are such an idiot. You have no right to complain or call the diagnosis "hooliganism."

      Now go to school and see if you can learn to read for comprehension. If you cannot learn, then just shut up so that you stop ridiculing yourself.

      Delete
    29. chris wallis,
      How am I wrong? I am not familiar with "objective nested hierarchies". Do you have more details?

      bwilson295,
      Whatever works for you... As long as you keep an open mind...

      photosynthesis,
      You're worse than Al-Qaeda when someone insults the prophet. Since you're a fanatic idiot and a retard animal, we're through.

      Delete
    30. Dan wrote:
      "If it looks designed, it is designed unless you have proof to the contrary."

      Ah, now that's where you take a wrong turn. You say stuff looks designed thus god-did-it. It's up to you to give proof that indeed a god(s) did it. That's how science works, you come with an idea, you need to provide evidence in favor of this idea.

      "You do agree that life looks designed, right?"

      Lets say for the sake of argument, I agree. My next question would be, do tell Dan, which designer is responsible for this design? What evidence do you have to support your claim it's designer (aka god(s) ) A, but not designer B.
      You can hide behind: for ID it isn't important to know which designer did it, but wouldn't you like to know which one did it? I know I would. If I were religious I wouldn't like to find out to be worshipping the wrong designer, if another designer was responsible for the universe as we see it today.

      Anyway, you want to have a go at providing evidence to support your claim? I've asked this simple question to many creationists and up until now, nobody has managed to answer it. They seem to think "evolution can't do X/ Y/ Z, thus god-did-it" is sufficient. It ain't.

      Good luck!

      Delete
    31. I am not sure what you find so unbelievable. You don't think transportation taxonomic groups fits neatly and completely inside other taxonomic groups ("Nested hierarchy")?

      No, I don't. That's why I'm asking you to show that they do, by actually creating such a taxonomy.

      Grouping by brand is misleading as you don't have brands in organisms.

      That's exactly the point. Cars do have brands, so you have to be able to fit them into the nested hierarchy, just as you have to do Takata airbags, and the other brands of airbags that will be used in various models.

      The reason they have brands is because they were individually designed, and didn't arise thru common descent.

      Is it starting to sink in why your claim is false? Biological taxonomists don't get to say "Oh, that doesn't fit in any nested hierarchy, so we'll just pretend it doesn't exist", so you don't get that luxury, either.

      Time to put up and or shut up, danbaur.

      Delete
    32. Ed,
      The argument for ID is from belief, but you wrongfully claim your's is not. If you admit yours is from belief, we're done. If not, the burden is on you. God cannot be scientifically proved or disproved. Agreed?

      Don't clutter your mind with designer A or B or if A = B. Baby steps first.

      It definitely has nothing to do with "evolution can't do it". To the contrary, our experience is that everything that looks designed is designed. I don't even know where one would come up with the opposite conclusion without a single example of positively not designed that looks designed.

      lutesuite,
      I am not sure what you're asking and why you're angry. Cars don't lay eggs either, so obviously you can take the example only so far. If not good enough for you, so be it.

      The whole "nested hierarchy" thing is an artificial construct anyway. Your argument is weak if it hinges on this construct.

      Delete
    33. lutesuite,
      I am not sure what you're asking and why you're angry. Cars don't lay eggs either, so obviously you can take the example only so far.

      The whole "nested hierarchy" thing is an artificial construct anyway.


      It seems you don't even understand the argument you were trying to make. If the nested hierarchy was an artificial construct, then you should be able to apply it to cars. That cars don't lay eggs shouldn't matter.

      That you admit that cars cannot be fit into a nested hierarchy shows your claim is false, and that the NH is not just an artificial construct. You might as well just admit the failure of this argument, and then try explain why the nested hierarchy exists if life was "designed." Good luck with that.

      Delete
    34. Insect wings, bird wings, and bat wings are examples of convergent evolution. They are all structures that evolved for flight.

      The problem with your statement is that you say they have been used as examples of gene transfer (HGT). They're not examples of HGT (though that doesn't mean no one ever used them thus), and as far as I can tell from a quick search through it, Wikipedia didn't say they are.

      How do we know they're not? Insect wings, bird wings, and bat wings differ greatly in their underlying structure. They're flaps of chitin (insects), feathers supported by arm bones with reduced fingers (birds), and a skin flap supported by arm and long finger bones (bats).

      Delete
    35. danbaur,

      "You're worse than Al-Qaeda when someone insults the prophet."

      The "slight" difference is that you insulted your own intelligence. How's it my fault if you decided to play the role of an authentic idiot?

      "Since you're a fanatic idiot and a retard animal, we're through."

      Now you're projecting. We were through the moment you decided to talk out of your ass, rather than read those explanations for comprehension. After that what could be the point of explaining things to you any further? If you can mistake insect wings with bird wings with bat wings so much that you don't understand why we would notice that they're convergent, rather than homologous, then there's not much anybody can do to help you. We're left with nothing else to do but point at your astounding stupidity.

      Delete
    36. lutesuite,
      "That you admit that cars cannot be fit into a nested hierarchy shows your claim is false, and that the NH is not just an artificial construct." - I don't know how you came up with this but it doesn't make any sense. It seems you're yet another incoherent fanatic, so there's no point continuing the discussion with you.

      bwilson295
      Never mind. That was just some text from Wikipedia I was using for other purpose that got badly misinterpreted. I didn't say those were examples of HGT.

      Delete
    37. danbaur,

      "To hold your world together you have certain beliefs too if you like to admit or not. Evolution is one of them that look very flimsy to me. Atheism is the other, right?"

      Atheism is not a belief. It is the provisional lack of belief in gods, there being no evidence of their existence.

      Delete
    38. It would seem that, for all his big talk about nested hierarchies, danbaur doesn't actually understand what a nested hierarchy entails. So it goes with creationists: The more they say about a topic, the less they know about it.

      Delete
    39. danbaur -

      I suppose then you are lying to yourself if you say you don't believe in Thor, Loki, Odin, Krishna, Shiva, Baal...?

      Delete
    40. a retard animal

      If gratuitously using an insulting term for the mentally handicapped is an example of the actions of a person whose morality supposedly comes from an infinitely loving and merciful God, please count me out.

      Delete
    41. danbaur,
      "You're lying to yourself."

      No, it was being honest with myself that led me to those conclusions.

      Delete
    42. Nice try at a dodge Dan, "If not, the burden is on you. God cannot be scientifically proved or disproved. Agreed?
      ", but hey, the burden of proof is still yours.

      Good luck.

      Delete
    43. Thanks Ed. Good luck to you too.
      to be continued...

      Delete
    44. danbaur,

      "to be continued..."

      Except you don't mean to continue. You've painted yourself into a corner, so you're done.

      You will be back with the same obfuscatory shtick later, pretending that this conversation never happened, and presenting your ideas as if they were new:(

      Delete
    45. danbaur,

      “The argument for ID is from belief….”

      I would challenge this idea. There are endless biological features that could not possibly be the result of natural selection acting on DNA replication failures. The pulley arrangement that allows the eye to rotate downward is a good example:

      “The body of the superior oblique muscle is located behind the eyeball, but the tendon (which is redirected by the trochlea) approaches the eyeball from the front. The tendon attaches to the top (superior aspect) of the eyeball at an angle of 51 degrees with respect to the primary position of the eye (looking straight forward). The force of the tendon’s pull therefore has two components: a forward component that tends to pull the eyeball downward (depression), and a medial component that tends to rotate the top of the eyeball toward the nose (intorsion).”
      https://en.wikipedia.org/wiki/Trochlea_of_superior_oblique

      Synchronized systems like this cannot be the result of random processes. It is just that simple.
      -
      “God cannot be scientifically proved or disproved.”

      I disagree with this as well. History recorded before the fact indicates that there is an authority managing human history who is not restrained by time.

      Delete
    46. Ed wrote

      "but hey, the burden of proof is still yours."

      If proponents of naturalism are going to argue that adequate answers exist without the need of a creator/intelligent designer, they are at least going to have to provide sufficient naturalistic explanations and reasons that top theism. By that i mean positive, compelling evidence that points to the fact that the natural world is self sufficient, and can have a origin by its own. They need good answers of how absolutely nothing magically can turn into something, or if they propose that the universe is eternal, and had no beginning, how we can reach now from eternity. If you add one event after the other starting now, whenever you stop, the timelapse will always be a defined timespan. You cannot reach eternity by adding one event after the other. Thats why there cannot be a past eternity, otherwise we would never reach now. Then the naturalist has to give good reasons of how randomness finetuned the expansion of the Big Bang, the fundamental forces, and hundreds of physical parameters, and the conditions to permit life on earth, how life can emerge from non-life through unguided, lucky events, and randomness was able to create the storage device, transcription and translation machinery , invent a optimal genetic code, translation code, and incalculable amount of precise instructions to create the first self irreducible complex replication cell, and millions of amazingly diverse species with the ability to evolve, and explain the emergence of conscient intelligent minds from inanimated matter ( quantum mechanics supports the idea that conscience/mind predates, and permeates all physical being.

      Delete
    47. If proponents of naturalism are going to argue that adequate answers exist without the need of a creator/intelligent designer, they are at least going to have to provide sufficient naturalistic explanations and reasons that top theism. By that i mean positive, compelling evidence that points to the fact that the natural world is self sufficient, and can have a origin by its own.

      Sure, if anyone is interested in defending metaphysical positions such as "naturalism." But if we're just sticking to science, then your position of "Goddidit" needs to be formed as a well-defined hypothesis, and then experimentally tested, just as with any other scientific claim. So any chance you or one of your fellow IDiots might someday at least attempt to do that? You can't just keep trying (and failing) to poke holes in evolutionary theory forever, you know.

      Delete
    48. txpiper,
      "There are endless biological features that could not possibly be the result of natural selection acting on DNA replication failures."

      You have no evidence to support this. Arguments from ignorance or personal incredulity are fallacious.

      Delete
    49. Chris B

      "Incredulous" basically means "I don't believe it". Well, there's a big difference between "not believing" that an actual animal, plant, phenomenon etc. *exists*, versus believing a certain "just so" story about HOW it came to exist.That is the THING that we are incredulous about - a *certain scenario* (Neo-Darwinism and abiogenesis , and that irreducible complex biological systems, and coded , instructed or specified complex information could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations and Natural Selection. The proponent of naturalism is "incredulous" that a intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists ? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things. ORIGIN is not the same as OPERATION. To study how biology works today, is entirely different from giving a *plausible* account of how it came about to be in the first place.

      Delete
    50. Chris B,

      "You have no evidence to support this. Arguments from ignorance or personal incredulity are fallacious."

      Hiding behind 'personal incredulity' is just a tactic that enables you to reside in Suckerville. If you want to actually apply your theory, and explain how you think the trochlea arrangement I referred to could be the result of DNA replication errors, feel free to elaborate. But I’m quite sure you will not. And were I you, I wouldn’t either for the same reason I wouldn’t defend the notion that someone rode a bicycle at mach 3. It is stupid.

      Delete
    51. OG,

      Don't pretend you have any respect for the scientific method and scientific integrity. I know you don't.

      That aside, you can't possibly call science a 'just so' story compared to your alternative of a supernatural creator, for which you have no evidence, and for which you have never attempted to produce evidence. You can't bullshit your way through with pseudoscientific nonsense. Never once have you presented any positive arguments for your alternative to science. You hide your god in the gaps of the scientific unknown, nothing more. Of course it is possible that a magical creator exists. Just provide the evidence. And be prepared to accept the implications that an intelligent designer of this universe would entail.

      txpiper,
      "Hiding behind 'personal incredulity' is just a tactic that enables you to reside in Suckerville."

      No, hiding behind personal incredulity is the logical fallacy you use to avoid facing reality (=living in Suckersville). You understand less about science than OG.

      Either one of you, if you think creationism/ID is a scientific alternative to evolutionary theory, please explain which of these things is intelligently designed, and how you know it is ID:

      1. a diamond
      2. Plasmodium falciparum
      3. The Grand Canyon
      4. Balaenoptera musculus
      5. Hapuna Beach, Hawaii

      Ok, go!

      Delete
    52. Chris B,

      "No, hiding behind personal incredulity is the logical fallacy you use..."

      Nope. I gave you a specific biological feature. I'll help you along if you don't understand how it works. It is your turn to apply your theory (and you are not going to do it).

      You really need to study how biological things actually perform before you declare that they are accidental accomplishments. You (and pompous dipwads like lutesuite and Diogenes) have been trained to be deliberately obtuse. You are not accomplished at real science. You’ve only mastered the skill of hiding behind canned responses, one of which is to change the subject. It is your theory. Show me how it works.

      Delete
    53. Tx, OG, Dan,
      first things first, could you three, and while you're busy take Robert along, decide which hypothesis you guys defend when it comes to the one creation hypothesis is true? And like science, also produce evidence why only this one creation hypothesis is true.

      Anyway, Tx and OG, you guys claim (your strawman version of) evolution can't have produced complex features. Unlike in politics where you can claim Trumpian bullshit and expect the opponent to produce proof your bullshit is in fact bullshit, in science you need to support your claims with evidence. In fact in a courtroom the DA needs to provide evidence someone indeed committed a murder. The defense can't claim "the police didn't provide evidence all other people on this world are innocent, thus my client can't have committed this crime."

      Both of you claim "evolution can't do X/ Y/ Z, thus goddidit". Like a court case, you need to provide evidence to support "goddidit". In a 2005 court case the judge concluded that negative claims against evolution, doesn't mean an alternative (ID) is true. The defense can't claim the police didn't exclude the other 6 billion people of this murder, thus my client is innocent. Thus, you can't claim science needs to show goddidntdoit, or else goddiddoit.

      Good luck!

      Delete
    54. txpiper writes:

      Hiding behind 'personal incredulity' is just a tactic that enables you to reside in Suckerville.

      ...and the Irony Meter of every Sandwalk reader immediately explodes.

      Delete
    55. It is your theory. Show me how it works.

      Easy, chance and necessity. All else is commentary. Now go and learn it.

      (Hat tip to the Talmudic story of Rabbi Hillel and the skeptic. You've read the Talmud, haven't you, txpiper, in order to understand the Old Testament and the religion Jesus professed his entire life on Earth?)

      Delete
    56. Ed wrote:

      "Both of you claim "evolution can't do X/ Y/ Z, thus goddidit"."

      i would apprechiate if you would not make a false portray of the logic i apply in my arguments.

      If you google: Confirmation of intelligent design predictions

      you will find following :

      Coded Information which is complex and instructional/specified found in epigenetic systems and genes, and irreducible , interdependent molecular machines and biosynthetic and metabolic pathways in biological systems point to a intelligent agent as best explanation of their setup and origins.

      Feel free to top my argument with naturalistic explanations....

      Delete
    57. Chris wrote:

      "Don't pretend you have any respect for the scientific method and scientific integrity. I know you don't."

      I do. But as Paul Nelson succintly points out:

      The inductive sciences (by which we might understand physics, chemistry, and the other primarily experimental sciences) are motivated by the question "How does nature normally operate?" The historical sciences (by which we might understand cosmology, geology, paleontology, evolutionary theory and biological systematics), on the other hand, are motivated primarily by the question "How did this system or object come to be?" These are logically distinct questions. In the latter case, when we ask how something came to be, we explain by invoking causal narratives or patterns of events -- employing methods often termed "abductive" or "retroductive" -- to find that set of events that best accounts for the features of what we observe in the present.

      This is "detective-style reasoning", and while such reasoning certainly employs natural laws (the bread-and-butter of the inductive or experimental sciences), those laws are insufficient tools for answering the questions posed in the historical sciences. The point has been appreciated well by evolutionary theorists defending their domain against the skepticism of their more experimentally-minded colleagues. In evolutionary theory, says Stephen Jay Gould, "we infer history from its results."

      Delete
    58. Synchronized systems like this cannot be the result of random processes. It is just that simple.

      This is so utterly pathetic. What you call a "synchronized process" is just another example of a simple "chicken and egg" formulation: You can't have chickens without eggs, but you can't have eggs without chickens, so God.

      This isn't a problem for evolution, it's a problem with your personal understanding of how systems and populations evolve. If you want to see an everyday example, just look at language. How did we get from Old English to Middle English to Modern English? Some central authority directing everyone to change how they talk? Two people suddenly speaking Modern English who gave birth to all the other Modern English speakers? Do you believe in the Tower of Babel story?

      Nope, it was just mistakes and other changes in common language usage by the population at large. Given some time, that caused all the million or so words and the complex rules for using them of Modern English.

      Delete
    59. OG & txpiper,

      More cut and paste obfuscation, rather than an answer to my question. Does ID/creationism have an answer to the question? You two sure don't know. About what I expected.

      Delete
    60. I have to quote Otangelo's attempt to provide scientific evidence for "Intelligent Design", because it is just too priceless:

      Coded Information which is complex and instructional/specified found in epigenetic systems and genes, and irreducible , interdependent molecular machines and biosynthetic and metabolic pathways in biological systems point to a intelligent agent as best explanation of their setup and origins.

      How can someone be so stupid as to think that collection of blind assertions actually constitutes scientific evidence? It boggles the mind.

      Delete
    61. OG,

      ""Don't pretend you have any respect for the scientific method and scientific integrity. I know you don't."

      I do."

      It's not only that you have no respect for science. It's even worse than that. You are only interested in understanding science insofar as you can use it to prop up your indefensible beliefs. Your cut and paste shtick is just quote mining, a cynical and gross abuse of science.

      txpiper,

      "Nope. I gave you a specific biological feature. I'll help you along if you don't understand how it works."

      The answer is in OG's post here: Otangelo Grasso Monday, December 19, 2016 7:20:00 AM. See if you can figure it out. If you bothered to actually learn evolutionary theory, you might gain some insight to your problem as well.

      "You really need to study how biological things actually perform before you declare that they are accidental accomplishments."
      A false characterization of evolution.

      "You (and pompous dipwads like lutesuite and Diogenes) have been trained to be deliberately obtuse."
      The projection here is astounding, even pathological. You just can't answer a question, can you?

      "You are not accomplished at real science."
      I do real science every day. That is where I am off to now. See if you can come up with an answer to my question.

      Delete
    62. Judmarc wrote:

      "What you call a "synchronized process" is just another example of a simple "chicken and egg" formulation: You can't have chickens without eggs, but you can't have eggs without chickens, so God.

      This isn't a problem for evolution, "

      Yep. The blind belief that evolution is the all powerful solution for everything in biology. Except when it isn't.

      As i have pointed out more than once, you cannot argue evolution prior when dna replication was setup, upon which evolution depends.

      Delete
    63. Judmarc,

      “What you call a "synchronized process" is just another example of a simple "chicken and egg" formulation…”

      I called it a ‘synchronized system’, because that’s what it is. A ‘synchronized process’ is what your theory needs, but all you have is accidents, which is no process at all.

      You’re correct about this being a chicken-egg problem. A random cartilage formation in the eye socket would not confer any kind of advantage. Neither would a useless superior oblique muscle. So I can’t blame you for not wanting to talk about how random DNA replication errors managed to thread a specialized muscle through a strategically positioned pulley. If I believed in sappy things like that, I’d rather talk about language development.

      Delete
    64. you cannot argue evolution prior when dna replication was setup, upon which evolution depends

      In response to my remarks that these objections to evolution are nothing more than pathetic variations on the old "chicken and egg" problem, Otangelo profoundly responds with - another "chicken and egg" problem!

      Logical problem-solving not a strong suit, Otangelo? (Otangelo of course is the unintentionally comedic holder of at least two strong self-contradictory opinions about why evolution didn't happen: First, that primitive life forms were "front loaded" to pass genetic information to their descendants; and second, that these descendants had no ancestors! I don't think Otangelo has realized the problem yet, but let's give him a few years.)

      Delete
    65. Judmarc

      maybe the creator made living beings each of its kind, whith the amazing hability of adaptation.

      Where is the comedy in holding this view of how things began ?

      And , no, you have not explained how cells emerged by natural means. And neither you will, unless if you do, your answers will be ridiculous nonsense just so stories.

      Get accostumed that a 747 does not emerge by chance. Nor a book. Nor cells and life.

      Delete
    66. Where is the comedy in holding this view of how things began ?

      Because it is ridiculous to see someone unquestioningly believe aspects of young earth creationism and old earth creationism just because they are both supposed alternatives to evolution, and never realize that they flatly contradict each other.

      Delete
    67. Judmarc

      YEC and OEC are not alternatives to evolution. There is no dispute between creationsim and evolution or science generally speaking. Unless you are more specific, and explain what exactly you mean by evolution.

      - If you argue about common ancestry and macro evolution of first speciation, than this hypothesis ( no, its NOT a theory ), competes with creationism/ID.

      But the dispute is broader, between random, nonguided lucky events creating all physical being, and a creator using his will , power, and information.

      My inference of design is not based on unquestioned blind belief, but solid , overwhelming scientific evidence which points CLEARLY and without any doubt to design as the far best explanation of origins.

      How could/would you EVER want to compare NOTHING as causal power to INTELLIGENCE ???!!

      Put your crutches of evolution away for a moment, and reflect about that...... :

      the most complex molecular self replicating factory arising by non guided, luck , random events.

      How insane is that ?

      Yes, its FAR FAR less likely than Large Hadron Collider coming to be by a lucky accident.

      Delete
    68. OG,

      Why don't you use your solid overwhelming scientific evidence to answer my question? Which things on my short list above were intelligently designed, and what predictions of intelligent design theory supports your decision?

      Delete
    69. My inference of design is not based on unquestioned blind belief, but solid , overwhelming scientific evidence which points CLEARLY and without any doubt to design as the far best explanation of origins.

      Your "inference of design" is based on your being too stupid to know your ass from a hole in the ground, Otangelo.

      Delete
    70. Otangelo:
      "But the dispute is broader, between random, nonguided lucky events creating all physical being,"

      I do remember mentioning you were attacking a strawman (version of evolution) in earlier posts, here it is again, well done!

      "and a creator using his will , power, and information."
      So it's a creator now, not a designer? Which one? His? How do you know?
      If I were religious I wouldn't like to find out I've been worshipping the wrong god/ designer/ creator. Thus the first and foremost question I'd want to have answered is which god/ designer/ creator we're talking about.

      Delete
    71. Ed,

      "which god/ designer/ creator we're talking about"

      Narrow the field. The one who creates and atones.

      Delete
    72. Tx, yes, thanks for the non-answer.

      Do you want a 3rd try at "which god/ designer/ creator are we talking about?"? Or can we expect another dodge, another non-answer?

      Delete
    73. Chris B asked:

      "Which things on my short list above were intelligently designed, and what predictions of intelligent design theory supports your decision? "

      My special brand of theism and its book says in the first versicle:

      In the beginning God created the heavens and the earth.

      that answers your first question.

      and in regard of ID predictions, what about you google :

      Confirmation of intelligent design predictions.

      Yes, i know, you will complain now that i did not answer specifically how ID predicts pathogenic viruses. You can also ask in a broader sense why God permits evil.
      The theodicy problem is one of the most difficult to answer.
      I have not answers to all questions you might ask.
      I like Rich Deems website where he gives in my view good answers to these questions:

      Where is God When Bad Things Happen? Why Natural Evil Must Exist

      http://www.godandscience.org/apologetics/natural_evil_theodicity.html

      Lutesuite

      are you having fun behaving as a housekeeping troll, like a clown ? Thank Larry which seems to amuse himself with you.

      Delete
    74. Oh, Otangelo. Is there any limit to the depths of your stupidity? You write:

      My special brand of theism and its book says in the first versicle:

      In the beginning God created the heavens and the earth.

      that answers your first question.

      and in regard of ID predictions, what about you google :

      Confirmation of intelligent design predictions.

      Yes, i know, you will complain now that i did not answer specifically how ID predicts pathogenic viruses.


      Here, again, is the list of things Chris B. asked you about:

      1. a diamond
      2. Plasmodium falciparum
      3. The Grand Canyon
      4. Balaenoptera musculus
      5. Hapuna Beach, Hawaii

      Now, which of those do you believe to be a "pathogenic virus"? LMAO!

      That's without even mentioning the fact that your idea of ID science involves consulting the "versicles" of a holy book. Oh, but ID is not religious, you say? LOL!

      Delete
    75. YEC and OEC are not alternatives to evolution. There is no dispute between creationsim and evolution or science generally speaking.

      I agree YEC and OEC are not alternatives to evolution and there is no dispute with the science, in the sense that evolution is science and YEC and OEC aren't real alternatives, scientifically speaking.

      But to get back to the point about what's comedic, it's that you strongly hold positions from YEC and OEC that are completely contradictory to each other, and it's fine with you to hold on to this incoherent soup of ideas as long as they all try to dispute evolution. From YEC you get the ideas of "kinds" and "no ancestors," that absolutely contradict the OEC idea of "front loading," which admits and depends on common ancestry.

      The whole notion of the Creator's job is entirely different between YEC and OEC. In YEC the job of creation is performed once and for all. In OEC, the Lord needs to step in and tweak things from time to time when "the edge of evolution" is reached. They're totally different, contradictory (and completely made up) ideas, and you don't even realize it.

      Delete
    76. OG,
      "My special brand of theism and its book says in the first versicle:

      In the beginning God created the heavens and the earth.

      that answers your first question."

      That's not science, that's religious belief.

      "and in regard of ID predictions, what about you google :

      Confirmation of intelligent design predictions."

      I'm sure if you resorted to your origins of life dodge and I responded with an invitation to google the current state of scientific knowledge on the subject for yourself, you would be perfectly satisfied with that answer, right?

      Do you really want to get into theodicy, because the implications of ID for the nature of the designer are both frightening and unavoidable.

      Delete
    77. OG,

      "Where is God When Bad Things Happen? Why Natural Evil Must Exist"

      But you reject naturalism as an explanation for the existence of the Universe and life here on Earth. You claim it was intelligently designed. So there is no 'natural' evil, there is only 'designed' evil.

      Delete
    78. Judmarc wrote:

      "and it's fine with you to hold on to this incoherent soup of ideas as long as they all try to dispute evolution. "

      As said previously, you need to define what you mean with evolution. What is disputed, is common ancestry, and macro-evolution of first degree os speciation. Second degree of speciation is a observed fact.

      Neiter OEC, nor YEC agrees with these two points.

      Maybe the common meaning of "front loading" is different than i used. I just meant what Shapiro says, namely that the hability of adaptation to the environment is a pre-programmed process.

      I do not stick neither to OEC nor YEC ( despite its my preference ) , since i do not understand all data available, specially in geology, to have a informed opinion.

      Delete
    79. "But to get back to the point about what's comedic, it's that you strongly hold positions from YEC and OEC that are completely contradictory to each other,"

      But OG has a 'natural' defense against contradictions, he calls them 'personal opinion'. Thus parts of his holy book are personal opinion, other parts are things he abides by.
      In the same way he reads his holy book, he reads science blurbs. One liners which fit his needs, he quotes mines and calls scientific evidence in favor of design. Even if in the same paper/ book/ blurb the author writes creation myths are myths indeed or somethings which contradicts OG's needs, OG invokes the personal opinion defense.

      It's like a lawyer claiming "evidence of the police which points to his client having murdered somebody" being mere "personal opinion".

      Delete
    80. Even when you think you've read it all, OG pulls even more new factoids out of his ... hat:
      "What is disputed, is common ancestry, and macro-evolution of first degree os speciation. Second degree of speciation is a observed fact. "

      WTF is second degree of speciation?

      Delete
    81. What is disputed, is common ancestry, and macro-evolution of first degree os speciation. Second degree of speciation is a observed fact.

      Neiter OEC, nor YEC agrees with these two points.


      Sorry Otangelo, you blew it again. OEC does admit to common ancestry, with just a bit of tweaking by the Deity every so often.

      James Shapiro does not profess "front loading" in the least. What he believes is that bacteria *themselves*, with no help from any deity, are capable of directing their mutations in ways favorable to their *evolutionary adaptation*. From everything you've ever said here, you don't agree with anything Shapiro thinks.

      It's just as I said previously: You've got a soup of half-baked, contradictory ideas swimming around your head about evolution with no rhyme or reason to it. You just know you don't like the idea of evolution, i.e., species arising without the necessity for a deity to oversee it all.

      That's fine, none of us cares if you want to be ignorant of the science. But you're not accomplishing anything at all by spewing this nonsense at an audience that includes scientists who do this stuff for a living, except reinforcing the idea that the sort of person who disbelieves evolution is someone ignorant of the science and not very capable of logical reasoning about it - someone very much like you, Otangelo.

      Delete
    82. OG wrote, "I do not stick neither to OEC nor YEC ( despite its my preference ) , since i do not understand all data available, specially in geology, to have a informed opinion."

      Odd. That's never stopped him before!

      Delete
    83. I wonder what Otangelo thinks of that fact that one of his heroes, Micheal Behe, accepts common descent as obviously true.

      https://en.wikipedia.org/wiki/Michael_Behe#Darwin.27s_Black_Box

      Delete
    84. This comment has been removed by a blog administrator.

      Delete
    85. @Otangelo Grasso

      This is your last warning. Learn how to use quotation marks (or italics) to identify material you did not write. It's not that hard.

      Delete
    86. This comment has been removed by the author.

      Delete
    87. This comment has been removed by the author.

      Delete
    88. I wonder what Otangelo thinks...

      The answer to any question of that form is quite easy, and is in the negative.

      Delete
    89. @Larry Moran

      The post you deleted was perfectly clear. There was no justification to delete it. Neither the last other two. Your acusations were not justified either. I have no need to plagiarize. Neither here, nor at my forum, nor anywere else. I was VERY patient, tolerating your behavior as moderator, vandalizing and deleting my posts without real justification.

      At the mean time, you find it perfectly fine, when trolls and clowns make personal attacks.

      Anyway, it was fun here. This was a great venue to expose the bankrupcy and irrationality of naturalism.

      Delete
    90. Learn how to use quotation marks (or italics) to identify material you did not write. It's not that hard.

      I guess it is too hard, for some people.

      Delete
    91. Otangelo kvetches to the bitter end:

      At the mean time, you find it perfectly fine, when trolls and clowns make personal attacks.

      "Personal attacks"? Like calling people "trolls and clowns", for example?

      If that really is your last post, how fitting that it highlights yet again your breathtaking hypocrisy and lack of self awareness.

      Delete
    92. OG,

      "Anyway, it was fun here. This was a great venue to expose the bankrupcy and irrationality of naturalism. "

      Please don't play the martyr. No one is buying it. What you have exposed is your inability to answer questions about ID/creationism. I never did get an answer about how you scientifically determine how things are ID. There is nothing irrational about naturalism. What is irrational is believing a supernatural being intelligently designed the Universe, and expect people to agree with you without producing any evidence of how you know this.

      Delete
    93. This is the way it always goes. The IDiots talk a great game about the new methods they've discovered to detect "design" (Complex specified information! No free lunch! Explanatory filter! Irreducible complexity!). But when challenged to actually demonstrate the utility of these methods in real world situations, they don't even try. Here are a couple prominent examples:

      Take the Intelligent Design Challenge!

      The Intelligent Design Challenge-Denouement


      My Life as Mathgrrl

      Delete
    94. "WTF is second degree of speciation?"

      A misdemeanor?

      Delete
    95. I was VERY patient, tolerating your behavior as moderator

      Wait, you as a *guest* "tolerated" your *host's* behavior?

      Delete
  5. bwilson wrote:

    "It does cause us to be totally amazed and awestruck by what the simple processes of mutation, genetic drift, and differential reproduction accomplish. "

    i am rather amazed that people with normal intelligence simply parrot hear say from " authorities " without giving a second thought, as if the assertions of these " experts " were true, without checking by themself.

    That said: bwilson : what research have you done that made you conclude , mutation, genetic drift, and differential reproduction ( sounds sciency, doesn't it ?!! ) have these amazing creative powers. I bet , neither you, nor Larry, not anyone else at this blog have the slightest evidence to back up the claim. Prove me wrong.

    ReplyDelete
    Replies
    1. Ontangelo,

      What do you think produces the observed physical differences between humans and chimps? Isn't it the DNA sequence differences that we see when we compare those genomes?

      Delete
    2. Eric

      Transposable element insertions.

      you can also google : Chimps, our brothers ?

      Delete
    3. Otangelo,

      Transposon activity is random mutagenesis. It is a permanent change in DNA sequence (mutation) that is random with respect to fitness.

      Delete
    4. Once again, Otangelo can't even keep his own story straight.

      Human and chimps could only exist if they were each separately and specially created by God.

      No, no, that's not true! Humans and chimps can each arise from a common ancestor thru random insertion of transposable elements.

      Which is it, Otangelo? Or are you too stupid to even realize the blatant contradiction of your position?

      Delete
    5. OG, I have two responses about how my research leads me to accept evolutionary processes as producing biodiversity.

      First, I have a deep understanding of the diversity of certain groups of animals (mostly birds) and plants (especially grasses and sedges). As I study them, I see the same kind of problems that Darwin faced with his barnacles and his friend Hooker faced with New Zealand plants. Many species are clearly distinct and some populations are clearly conspecific even if they are variable, but some groups of organisms are intermediate. Are they different or not? How could they get to be this way? Darwin's ideas, greatly expanded by later researchers, explain what I am seeing and help me understand it.

      People who really know the classification of some group of species well will understand this. Nothing in your voluminous writings suggests you will.

      Delete
    6. A second, smaller subject is the variation in duplicated genes. I've worked with diploid taxa that have an occasional duplicated gene, with many tetraploids, and with a genus of diploidized ancient polyploids.

      I observed something interesting. In general, one copy of the duplicated gene makes a fully functional protein and has little variation. The second copy might make the same version, but often it makes two or more modified versions. In general, least one of these is less active (under the experimental conditions) than the normal version made by the other gene copy. Sometimes, the protein made by one copy doesn't work at all. (I suspect this is often true, but I could only detect cases where both genes made functional copies most of the time; limitation of my experimental setup.)

      This fits very well with the idea that duplicated genes (from polyploidy or small duplication events) can change, with one eventually producing a different enzyme than the original version. I could only detect small changes with my experimental set-up, but there's no reason large changes can't happen by the same mechanisms.

      This process of change in duplicated genes can produce small changes in, for example pH tolerance, or major changes in body plan (e.g. by duplication of Hox genes).

      Delete
    7. bwilson295

      there are no intermediates between prokaryotes and eukaryotes:

      ― Alan H. Linton

      “Throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another... Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic [i.e., bacterial] to eukaryotic [i.e., plant and animal] cells, let alone throughout the whole array of higher multicellular organisms.”

      The organizational complexity of the eukaryotes is so much greater than that of the prokaryotes that it is difficult to visualize how a eukaryote could have arisen from any known prokaryote (Hickman et al., 1997, p. 39).

      The next major hurdle is the transition from unicellular to multicellular life.

      You can google : Unicellular and multicellular Organisms are best explained through design

      The cells had not only to hold together, but important mechanisms to stick the cells together had to emerge, that is, the ability of individual cells to associate in precise patterns to form tissues, organs, and organ systems requires that individual cells be able to recognize, adhere to, and communicate with each other. The apparatus of cell junctions and the extracellular matrix is critical for every aspect of the organization, function, and dynamics of multicellular structures.

      Secondly: Three factors account for the extraordinary sensitivity of signal transducers: the high affinity of receptors for signal molecules, cooperativity (often but not always) in the ligand-receptor interaction, and amplification of the signal by enzyme cascades. The trigger for each system is different, but the general features of signal transduction are common to all: a signal interacts with a receptor; the activated receptor interacts with cellular machinery, producing a second signal or a change in the activity of a cellular protein; the metabolic activity of the target cell undergoes a change; and finally, the transduction event ends. This seems to be a irreducible system, requiring high content of pre-programming and advanced coding.

      Furthermore: Like engineers carefully blowing up a bridge, cells have intricate, programmed suicide mechanisms. Without apoptosis, all multicellular life would be impossible. Good luck to proponents of evolution to explain how it emerged........

      Delete
    8. Then you cannot explain the sudden appearance of various complex organisms, like we observe in the Cambrian explosion.

      Furthermore , irreducible complexity shows that a gradual evolutionary development of eyes ( trilobite eyes, the most advanced known, appear suddenly in the cambrian ), hemoglobin, hemopoietic stem cells, toxic snakes, etc. is not possible.

      The creation model seems to me to make most sense. A "small" number of different phyla were created at the beginning, and each diversified into various treelike branches through microevolutionary steps. HGT does not explain the hudge differences between prokaryotes and eukaryotes.

      Delete
    9. Eric wrote:

      "Transposon activity is random mutagenesis. It is a permanent change in DNA sequence (mutation) that is random with respect to fitness."

      Following paper :

      Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

      says different :

      Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion.

      Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition.

      This is evidence of reproducible, nonrandom biochemical events, and is an indication that these shared sequences are not due to common ancestry, but DESIGNED reproducible biochemical events.

      Delete
    10. Hey Otangelo,
      can you show me *exactly* where the author of this paper concludes something was "DESIGNED". Because I can't find this conclusion anywhere in the paper...

      Delete
    11. Ontangelo,

      "Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion."

      Please reread my post. In it you will find the following phrase:

      "random with respect to fitness"

      Nothing you presented challenges that conclusion. Even with insertional hotspots you will still get a whole range of changes in fitness, from very deleterious to neutral to beneficial. The mechanisms of transposon activity are not able to specifically create a beneficial mutation in response to a specific environmental stimulus. That is what makes these mutations random in the original meaning of "random mutations".

      If you go back to the first papers that define random mutation (plate replica experiment and the fluctuation experiment) they define random as being random with respect to fitness. These experiments were done in the 1950's, so they didn't even understand the properties of DNA at that time. What they found is that the processes of mutations were blind to the needs of the organism, and that is what is meant by random mutation.

      Delete
    12. I do know better than to respond to OG, I really do. But sometimes I do it anyway.

      OG asks what I've learned that myself that leads me to think that evolution is true. I answer. OG changes the subject to say there's no evidence of transition from prokaryotes to eukaryotes (though he's had the evidence explained to him many times) and to bring up several more topics that he seems to imply I should explain.

      This is so typical of OG that I shouldn't complain. I should just not keep responding.

      Delete
    13. It's like picking a scab, isn't it, bwilson295?

      Delete
    14. Yes, it is, Lutesuite. Hard not to, and yet not helpful.

      Delete
  6. Replies
    1. ...asks the guy who can't think, period.

      Didn't you read Eric's last post? Was it too difficult for you to comprehend?

      Delete
    2. Eric wrote

      " The mechanisms of transposon activity are not able to specifically create a beneficial mutation in response to a specific environmental stimulus."

      Bollocks.

      We know from an extensive literature on insertional mutagenesis in nature and the laboratory that introduction of a transposable element into a particular location CONFERS NEW FUNCTIONAL PROPERTIES on that region of the genome (Shapiro, 1983; Craig et al., 2002; Deininger et al., 2003).

      Delete
    3. Sorry, Otangelo. Appeals to authority mean nothing when the authority to whom you're appealing is an ignorant crackpot:

      http://sandwalk.blogspot.ca/2012/09/james-shapiro-claims-credit-for.html

      Delete
    4. That is false Otangelo, of the very many insertions, only a few have conferred functional "properties" to the genome, which is to be expected. Since there's so many insertions, sooner or later some functions had to arise.

      Delete
    5. I certainly can Otangelo, that's why I'm asking you where exactly the author claimed "DESIGNED" (note capitals). Because for some weird reason, I can't find the sentence where the author claims this...
      Want to try again?

      Delete
    6. This comment has been removed by a blog administrator.

      Delete
    7. Ahh, it's not the author of the paper who concludes "Designed", but you added it yourself. You neglect to mention where the quote in the paper ends and where you add your own things.

      "That seems to me to justify that it is a DESIGNED process. "

      Does it now? I'm very interested to know what proof you could bring forward for this conclusion? Did new TE insertions cause new genes to become active?

      But that's weird, because earlier on you said the genome was front loaded and thus has been deteriorating since the beginning.

      Now you claim it's not, because new genes and functions arise through TE insertions. Huh??

      Could you please try to decide what you belief in??

      Delete
    8. This comment has been removed by a blog administrator.

      Delete
    9. @Otangelo Grasso

      You have been warned repeatedly about plagiarism. You can't just copy and paste the words of other people without acknowledging the source and putting the words in quotation marks.

      What you're doing is dishonest and it could get me in trouble.

      I can't waste time checking all of your comments to see if you have plagiarized. If you don't stop I'll just have to delete everything you post.

      Delete
    10. Larry

      it happens that i left the webpage with the two last comments which you deleted open, so i was able to check.

      Its pretty clear in both posts what was coming from the papers, and what were my own comments.

      Your deletion was not justified.

      Delete
    11. Oh, really, Otangelo? Was it as clear as it was in this post, where you made it appear as if the authors claimed that shared sequences indicated that genomes were "DESIGNED"?

      Another example of Otangelo's lies

      Delete
    12. Otangelo,

      "
      We know from an extensive literature on insertional mutagenesis in nature and the laboratory that introduction of a transposable element into a particular location CONFERS NEW FUNCTIONAL PROPERTIES on that region of the genome (Shapiro, 1983; Craig et al., 2002; Deininger et al., 2003)."

      We also know that those same transposons insert elsewhere in the genome where they perform no function, or even have detrimental function. You can't focus on just the beneficial functions and pretend that the neutral and detrimental insertions don't happen.

      Delete
  7. I know it is irrelevant to the argument at hand, but the human (and other vertebrate) body actually produces many billions of different functional proteins. Almost all of them are antibodies or T cell receptors.

    Of course a vast majority of these proteins will never bind to an pathogenic antigen, but they sill must be considered functional. Their function is to have the potential to detect an unknown pathogen. If there were significantly fewer the immune system wouldn't work as well, so they all have a function.

    This is hardly new. In fact it is so old and well understood that people don't seem to think it counts as part of the "proteome", but that is arbitrary. Other proteins can't be more than a millionth of the total.

    It is unfortunate that the process for producing this diversity is not completely error free. It is especially unfortunate for me. I have a lymphoma caused (at least in part) by a heavy chain promoter mis-recombined to the BCL-2 gene.

    ReplyDelete
    Replies
    1. "Of course a vast majority of these proteins will never bind to an pathogenic antigen, but they sill must be considered functional. "

      Some of those proteins do bind to a pathogenic antigen. In the case of antibodies, the B-cells expressing the antibody go through a process called affinity maturation, where random mutations are introduced into the variable binding region of the antibody protein molecule. Cells containing random antibody variants that happen to bind more efficiently to the pathogenic antigen receive a proliferation signal and increase in number. Cells carrying variants that no longer bind the antigen or do so less efiiciently receive no or reduced proliferation signal, and dwindle to extinction in the cell population. Thus, through a process of random mutation and selection on variation, the body produces more specific antibody to better fight the pathogen. One might even claim the antibody was intelligently designed to fight the pathogen.

      Delete
  8. My random act of mischief:

    The evident nested hierarchy of mutation events in the of the GULOP gene sequence can be best explained per phylogenetic tree positing humans & chimps with a very recent common ancestor; whereas Humans/Chimps have a more distant common ancestor with the outgroup Macaques; while Gorillas and other primates are related to Humans/Chimps in a most predictable fashion (according to expectations of current evolutionary “theory”)

    This provides an opportunity where we can pose and juxtapose:

    Pose: Professor Larry Moran on the Human GULOP Pseudogene

    As opposed to Juxtapose: a fast and easy ID synopsis of how an accumulation of mutations in the GLU/GLO/GULO/GULOP locus represents an exaptation made possible by differential mRNA editing

    Two contrary questions may vex some present:

    1- Does the constellation of GULOP mutations indeed represent an adaptive exaptation? (Fast answer = Yes!

    2- Does differential editing of GULOP mRNA in fact rescue endogenous production of Ascorbic acid in fetus’ brains and breast-fed infants? (Fast answer: No – but not to hear the ID protagonists tell it.)

    In any case, the inactivation of the GULO gene may indeed have proven adaptive. for more elaborate reasons (than suggested by E.G. Calabrese) as explained in this easy to read summary from the BBC.

    ReplyDelete
  9. I'm not an expert on proteoforms by any means, but there does seem to be some really good evidence for some classes of proteins to have many many proteoforms. Histones in particular

    http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b01090
    http://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.6b00694
    http://www.sciencedirect.com/science/article/pii/S002196731630601X
    http://repository.topdownproteomics.org/Proteoforms?query=Q7L7L0

    In addition there seems to be approximately 140K human PTM's cataloged in the nextprot database

    https://www.nextprot.org/about/human-proteome

    There are also new technologies coming on line that are identifying hundred of thousands of modified peptides from bottom up human proteomics experiments

    http://www.nature.com/nbt/journal/v33/n7/abs/nbt.3267.html

    From what data I have seen, we are just scratching the surface of what is out there. This is pretty clear to anyone who actually does these types of experiments in the lab

    ReplyDelete
    Replies
    1. Brett: "There are also new technologies coming on line that are identifying hundred of thousands of modified peptides from bottom up human proteomics experiments"

      Uh, identifying, OK. But are they assayed or something so the modification is known to have a functional purpose, as opposed to just assuming "it exists in multiple forms, so all differences between them exist for functional reasons"? Some, I presume, exist at low levels and could just be necessary side-effects of synthesis processes.

      Delete
    2. Well I don't know, but there is a considerable amount of data that there are lot's of protoforms out there in biology. And it's been known for a long time that many of them have real biological functions (oxidation, phosphorylation, methylation, glycosylation just to name a few)

      and just because they are at low levels doesn't mean they are non functional.

      This is just one study of the phosphoproteome (there are many) which identified over 20K phosphorylated peptides and linked many of these low level modifications to biological activity

      http://stke.sciencemag.org/content/3/104/ra3.full

      Delete