Common Design vs. Common Descent

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I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

5,163 thoughts on “Common Design vs. Common Descent”

  1. colewd,

    So the paper you cited on sines as a phylogenetic sorting tool only shows animals with their own tree branch.

    So, you deny the use of transposable elements as phylogenetic markers at any level? As I have said before, you therefore deny their use in human relationships, since Alu sequences are used in such tests. You can’t get out of this by saying ‘humans can interbreed’.

    If an Alu or other SINE is present in a group of organisms at a particular site, the nature of transposition is such that they almost certainly all inherited it from a common ancestor. One does not need access to the DNA of that ancestor – or rather, one has it, at that site, in copy form. Barring HGT or site-directed bias, the common ancestor of a clade with a SINE at a site must have had that SINE too. It would be perverse to deny this.

  2. I was recce-ing a section of an ‘ultra’ race the other day that I’d be doing in the dark on the event itself. I came unexpectedly to a TV relay station in the woods, not where I thought it was. I puzzled over this for ages, none the wiser when I got to the pub, even asking a friend who lives nearby if they’d moved the station in the 25 years since my map was made … !

    It was more likely to me that a TV relay had been moved wholesale than that I could have made a mistake with my map-reading! I eventually twigged, of course it was me, but this seems similar to the situation here. When teams invest time and money to find 36 diagnostic SINEs, collect materials, design PCR primers, mine data banks, organise results objectively, write a paper, respond to referee criticisms, trying to resolve particular cladistic branches, it is more plausible to the Creationist that they are all – what? – dumb, ideologically motivated, misguided, dishonest fools? Not just colewd and Sal, but “I-accept-common-descent” Mung seem afflicted with this. Occam’s Razor needs a sharpening.

  3. colewd: The hierarchy becomes nested through the use of extinct animals.

    No, the hierarchy is nested because whales are mammals. They nurse their young, have three earbones involved in sound transmission, some species have hair at birth, they are mammals. They don’t have any features that would place them in other groups, even though some of them would be darn handy for an aquatic animal (gills!!!). If you do a phylogenetic analysis on genetic sequences they also nest within mammals.

    Whales are nested within mammals. The most parsimonuous explanation is that they descend from an ancestor that was also a mammal. If you want to make common design fly you need to find an alternative explanation.

    That, or deny that whales are mammals.

  5. Mung: My thoughts? That the evidence of design positively screams in your face. One has to work hard to deny it.

    Ya but… but… it’s only mine that count! 🙁

  7. Allan Miller: When teams invest time and money to find 36 diagnostic SINEs, collect materials, design PCR primers, mine data banks, organise results objectively, write a paper, respond to referee criticisms, trying to resolve particular cladistic branches, it is more plausible to the Creationist that they are all – what? – dumb, ideologically motivated, misguided, dishonest fools?

    It’s hard to believe that evilutionists are that passionate about not letting a divine foot in the door, what with all of the ancient aliens they’re busy hiding in museums and labs, the massive underground cities and highways they’re building throughout the US–all starting at area 51–the moonshots and moonrocks they’ve had to manufacture over time, the enormous efforts to fake the 9-11 controlled demolitions as if they were terrorist attacks, not to mention all of the humans and rabbits found in the precambrian that have to be reburied and “refound” as if they were much later and/or different organisms.

    But that’s just how much they hate Jesus. They hate baby Jesus even more.

    Glen Davidson

  8. keiths: Mung, too, is afflicted by the Jebus Effect.

    Jebus and the Holy Spittoon. Far superior to some silly flying spaghetti monster.

  9. Allan Miller: …it is more plausible to the Creationist that they are all – what? – dumb, ideologically motivated, misguided, dishonest fools?

    It’s the keiths effect.

  11. Corneel: I give it one week before this also becomes a guano-able phrase.

    🙂

    Posts sent to guano fall into a nice neat objective nested hierarchy.

  12. Rumraket: Mung: My thoughts? That the evidence of design positively screams in your face. One has to work hard to deny it.
    Ya but… but… it’s only mine that count!

    Darwin spent a lifetime on that project, and then thousands of people have devoted 150 more years to it.

    So technically, Mung is right, science is hard and takes a lot of work.

    Is this a problem?

  13. Corneel,

    No, the hierarchy is nested because whales are mammals. They nurse their young, have three earbones involved in sound transmission, some species have hair at birth, they are mammals. They don’t have any features that would place them in other groups, even though some of them would be darn handy for an aquatic animal (gills!!!). If you do a phylogenetic analysis on genetic sequences they also nest within mammals.

    I agree they all can be categorized as mammals because of similar features. Some live in the ocean, some on land, and some can fly. Some of the ones that live in the ocean and fly have echo location capability. The hierarchy does not seem very nested.

    Looks like a new design concept to me 🙂

  14. Allan Miller,

    Bill

    So the paper you cited on sines as a phylogenetic sorting tool only shows animals with their own tree branch.

    Allan

    So, you deny the use of transposable elements as phylogenetic markers at any level?

    Not sure how you got here.

    If an Alu or other SINE is present in a group of organisms at a particular site, the nature of transposition is such that they almost certainly all inherited it from a common ancestor. One does not need access to the DNA of that ancestor – or rather, one has it, at that site, in copy form. Barring HGT or site-directed bias, the common ancestor of a clade with a SINE at a site must have had that SINE too. It would be perverse to deny this.

    Or its location equivalence is the result of a common designer 🙂

  15. OMagain,

    So what you are saying is there is absolutely nothing we can do to expand our knowledge past the “fact” that convergent evolution was designed.

    I think Darwin gave us false hope of understanding origin of life and new life forms based on his inference. Now that we have molecular evidence of whats in the cell this hope is fading.

    As we do not have significant research studying the origin of matter, I think the origin of living organisms as a research project will fade away baring any new discovery that gives it more hope.

    I do think the demarkation of design and descent is an interesting subject.

  16. colewd: Or its location equivalence is the result of a common designer

    And, it’s a reset to initial settings once again.

    All of the explanations of the problems, and of the inability of “common design” to be more than a religious-styled vague analogy, has done nothing to even begin processing at a meaningful level, it’s all just a matter of common design.

    ID doesn’t aspire to our “pathetic level of detail,” because for a lot of people it doesn’t need to get beyond mouthing the words “common design.” Dembski’s razor means we shouldn’t go beyond the most simple-minded answer possible.

    Glen Davidson

  17. colewd: Or its location equivalence is the result of a common designer

    That doesn’t actually explain why they fall into a nested hiearchy. All you are saying here is “The designer deliberately made a nested hiearchy, which is only predicted by evolution”.

    Why, Bill?

  18. colewd: I agree they all can be categorized as mammals because of similar features. Some live in the ocean, some on land, and some can fly. Some of the ones that live in the ocean and fly have echo location capability. The hierarchy does not seem very nested.

    So in order to deny the nested hiearchy, you focus on a single instance of convergence and ignore that pretty much all other characters confirm the hiearchy. Why do you ignore all the other data? Why is there such consilience between independent phylogenies?

  19. Rumraket,

    So in order to deny the nested hiearchy, you focus on a single instance of convergence and ignore that pretty much all other characters confirm the hiearchy. Why do you ignore all the other data? Why is there such consilience between independent phylogenies?

    There is more than a single instance of convergence. As Mung would say, the phylogenetic data falls into a nested hierarchy except when it doesn’t.

    The hybrid of nested and non tested hierarchy look like the result of a well planned design.

  20. colewd: Now that we have molecular evidence of whats in the cell this hope is fading.

    That’s just the creationist propaganda-line you’ve been taught to memorize and regurgitate. “More and more scientists are leaving evolution”.

    Strangely enough, all the people who work in biochemistry and molecular biology are of the opposite opinion. That our understanding of the evolution and diversification of living organisms is ever so slowly becoming better all the time. I have given several references in this thread already to research projects using ancestral sequence reconstruction to discover the origin and evolutionary history of everything from enzymes and trancription factors, to structural proteins and the moving parts of molecular machines.

    From an interview of Eugene Koonin:

    Suzan Mazur: Are you saying this is the top discovery in evolutionary biology in the last 50 years?

    Eugene Koonin: The word “discovery” may not apply quite directly here. It’s a transformation of the whole science, which is based on a variety of discoveries. The very approach to evolutionary studies has changed completely. Not only the fact of evolution itself but the existence of deep evolutionary connections between different domains of life — to be concrete — evolutionary connections between, let us say, mammals, such as humans, and prokaryotes, bacteria and archaea, have become indisputable. These findings make questioning not only the reality of evolution but the evolutionary unity of all life on earth completely ridiculous and outside of the field of rational discourse.

    Then to be more specific, I would probably showcase the advances of metagenomics — you know, the genomic revolution continues in the sense that now through metagenomics scientists are able to obtain a less and less biased picture of the diversity and evolution of life on Earth. It’s becoming not so unrealistic to think about something approaching a complete picture of the evolutionary history of life.

    And then I would showcase something very specific. That is the latest discovery of the particular group of archaea that was the direct ancestor of eukaryotes. And in this case, “discovery” is the right word.

    There is a necessity to bring to the broader audience of biologists and lay public Mike Lynch’s reformulation of the principles of genomics in terms of population genetics. Paraphrasing the famous pronouncement of Theodosius Dobzhansky, one of the Founding Fathers of the Modern Synthesis [“Nothing in biology makes sense except in the light of evolution.”], Lynch wrote in one of his papers: “Nothing in evolution makes sense except in the sense of population genetics.” That is absolutely true. The details of population genetic theory are difficult to explain even to biologists who are not specially trained, yet we have to communicate these ideas to a broader audience, including the lay public, and in qualitative terms.

  21. colewd,

    Not sure how you got here.

    I dare say you aren’t, but that is the logical endpoint of your thought process. If you can’t infer common descent from SINEs because ‘you only have the ends of the tree’, then that logic must – logically – apply everywhere.

    If I have 3 sequences: flankSINEflank, flankSINEflank and flankflank, I cannot infer that the first two got their SINE sequences from a common ancestor not ancestral to the third, irrespective of the taxonomic separation, if your argument had any merit.

  22. colewd: Some of the ones that live in the ocean and fly have echo location capability.

    Made me wonder whether hippos have any abilities in underwater communication. Seems they do. (PDF)

    The most frequent sounds were underwater clicks,
    croaks and whines given without the expiration of air…

    ETA quote

  23. colewd,

    There is more than a single instance of convergence. As Mung would say, the phylogenetic data falls into a nested hierarchy except when it doesn’t.

    SINE data comes close to being free of homoplasy. So it provides a very useful cross-check. But you confuse molecular and phenotypic convergence. Do you seriously think convergence confuses us into thinking whales are closer to bats, because of echolocation?

  24. colewd,

    Or its location equivalence is the result of a common designer

    That’s just pathetic. If you troubled yourself to take up my suggestion of actually understanding SINE data, you might see why.

  25. colewd: Or its location equivalence is the result of a common designer 🙂

    Sounds like you are treading close to giving an actual design explanation, any evidence to support that there exists such a designer or its methods?

  26. Allan Miller: But you confuse molecular and phenotypic convergence. Do you seriously think convergence confuses us into thinking whales are closer to bats, because of echolocation?

    I don’t think he confuses either. He confuses a vague functional similarity (they both make noises and get information from the echoes) with the sort of detailed similarity that would potentially confound phylogenetic analysis. Since the only real resemblances between bat and whale echolocation are the name and gross function, there’s no implication that they’re homologous. But Bill isn’t interested in looking at data.

  27. Allan Miller,

    That’s just pathetic. If you troubled yourself to take up my suggestion of actually understanding SINE data, you might see why.

    An assertion, but as far as assertions go this is one of the best 🙂

  28. newton,

    Sounds like you are treading close to giving an actual design explanation, any evidence to support that there exists such a designer or its methods?

    Historical evidence.

  30. colewd: There is more than a single instance of convergence.

    Between bats and whales? Could you give examples? And even if there were 10 convergent attributes between bats and whales, tha still wouldn’t invalidate the nested hiearchy.

    As Mung would say, the phylogenetic data falls into a nested hierarchy except when it doesn’t.

    And the causes of why and when it doesn’t are well understood to be due to convergent evolution. And even then, they are are really just tiny instances of noise in a sea of signals confirming the nested hiearchy.

    The mere fact that bats and whales echolocate does not suffice to overturn the observation that every other aspect of these organisms confirm the nested hiarchy.

    The hybrid of nested and non tested hierarchy look like the result of a well planned design.

    Could you give a concrete real-world examples of such “well planned designs” that show an overwhelmingly well supported nesting hiearchy with the fantastically rare occurence of homoplasy?

  31. Rumraket,

    Could you give a concrete real-world examples of such “well planned designs” that show an overwhelmingly well supported nesting hiearchy with the fantastically rare occurrence of homoplasy?

    The line of Macintosh computers.

  32. John Harshman: Since the only real resemblances between bat and whale echolocation are the name and gross function, there’s no implication that they’re homologous.

    As far as I am aware this is technically not true. One of the proteins involved in hearing is actually remarkably convergent in amino acid sequence.

    Li Y1, Liu Z, Shi P, Zhang J. The hearing gene Prestin unites echolocating bats and whales. Curr Biol. 2010 Jan 26;20(2):R55-6. doi: 10.1016/j.cub.2009.11.042.

    Abstract
    Echolocation is a sensory mechanism for locating, ranging and identifying objects which involves the emission of calls into the environment and listening to the echoes returning from objects [1]. Only microbats and toothed whales have acquired sophisticated echolocation, indispensable for their orientation and foraging [1]. Although the bat and whale biosonars originated independently and differ substantially in many aspects [2], we here report the surprising finding that the bottlenose dolphin, a toothed whale, is clustered with microbats in the gene tree constructed using protein sequences encoded by the hearing gene Prestin.

    Creationists have been losing their mind about this paper ever since it came out. They haven’t read Theobald’s 29 evidences for macroevolution. If they had, they would have discovered this:
    Caveats with Phylogenetic Inference.

    Caveats with Phylogenetic Inference

    As with any investigational scientific method, certain conditions must hold in order for the results to be reliable. A common premise of many molecular phylogenetic methods is that genes are transmitted via vertical, lineal inheritance, i.e. from parent to offspring. If this premise is violated, gene trees will not recapitulate an organismic or species phylogeny. This assumption is violated in instances of horizontal transfer, e.g. in transformation of a bacterium by a DNA plasmid, or in retroviral insertion into a host’s genome. During the early evolution of life, before the advent of multicellular organisms, horizontal transfer was likely very frequent (as it is today in the observed evolution of bacteria and other unicellular organisms). Thus, it is questionable whether molecular phylogenetic methods are applicable, even in principle, to resolving the evolutionary patterns of many microbes, including early evolution near the most recent common ancestor of all living organisms (Doolittle 1999; Doolittle 2000; Woese 1998).

    The list below gives some of the more important caveats that scientists must keep in mind when interpreting the results of a phylogenetic analysis (Swofford 1996, pp. 493-509). In general, the contribution of each of these concerns will be “averaged out” by including more independent characters in the phylogenetic analysis, such as more genes and longer sequences.

    Correlated characters: each character used in the analysis optimally should be genetically independent. Characters that are strongly functionally correlated are better thought of as a single character. There are statistical tests that can help control for unrecognized character correlation, such as the block bootstrap and jackknife.

    True structural convergence: structures that have undergone convergent evolution can artificially result in incorrect tree topologies. Including more characters in the analysis also aids in overcoming convergent effects.

    Character reversals: characters that revert to an ancestral state pose a challenge similar to convergence. Because DNA and RNA only have four different character states, they are especially prone to reversals during evolution.

    Lost characters: lineages that have lost characters (such as whales and their hindlimbs) can also pose cladistic problems. Often, if a cladistic analysis indicates strongly that a certain character has been lost during evolution, it is best to omit this character in higher resolution analyses of that lineage.

    Missing characters: incomplete fossils are problematic, since they may lack important characters. Better fossils are the answer.

    Intractable number of possible phylogenetic trees: for computational reasons, this is one of the most important phylogenetic challenges to overcome. The goal of a phylogenetic reconstruction is to determine the best tree that the data supports. For an analysis of only five species, there are 15 possible trees. For an analysis of 50 species, there are over 1074 possible trees that must be searched—which is computationally impossible. This problem is not as bad as it first sounds, since narrowing down the number of reasonable trees can be trivial in many cases (for instance, using the branch and bound algorithm). Several methods have been developed to work around this issue successfully, and ultimately more powerful computers are better.

    Maximum Likelihood assumptions: the maximum likelihood method makes explicit assumptions about the pattern of nucleotide substitutions based upon a given model of nucleotide evolution. These assumptions are based upon a solid statistical foundation; however, the validity of the models must be considered when evaluating the results.

    Long branch attraction: lineages that diverged relatively long ago will tend to “cluster” together in a phylogenetic reconstruction under the appropriate conditions. The mathematical reasons are somewhat complicated, but using more slowly evolving genes (or regions of genes) helps overcome the problem.

    Rate variation between lineages: rates of nucleotide substitution may differ between lineages; this can contribute to long branch attraction and result in incorrect tree topologies. However, maximum likelihood and least squares methods are particularly useful here.

    Rate variation within a single gene: rates of nucleotide substitution can vary along the length of a single gene—this also exacerbates long branch attraction.

    Gene trees are not equivalent to species trees: from simple Mendelian genetics we know that genes segregate individually, and that throughout time individual genes do not necessarily follow organismic genealogy (Avise and Wollenberg 1997; Fitch 1970; Hudson 1992; Nichols 2001; Wu 1991). An obvious example is the fact that while you may have brown eyes, your child may have the genes for blue eyes—but that does not mean your child is not your descendent, or that your brown-eyed children are more closely related to you than your blue-eyed children. Including multiple genes in the analysis is a solution to this conundrum. Based upon simple genetic calculations, an analysis of more than five genes is usually necessary to accurately reconstruct a species phylogeny (Wu 1991).

    I have bolded the part Bill and all other creationists confused about convergence are missing.

  35. Rumraket: As far as I am aware this is technically not true. One of the proteins involved in hearing is actually remarkably convergent in amino acid sequence.

    Sort of. I’d like to see a better sample of whales. And it’s also true that if you use DNA sequences at synonymous sites, you get the standard tree.

  36. colewd,

    An assertion, but as far as assertions go this is one of the best

    Pathetic again. You just aren’t trying.

    There’s a long-running nonsense game on British radio program “I’m Sorry I Haven’t A Clue” (kinda appropriate) called “Mornington Crescent” (the name of a subway stop). There are no real rules, but once in a while someone says “Mornington Cresent” and gets points. That’s how you’re using “Design”. There’s no reason for it, it’s just that when you can’t think of anything to say, say that.

  37. More info on phosphorylation of proteins, and more reasons Common Descent needs a miracle.

    The phosphorylation site has to be distinct, it can’t be randomly assembled much like an address or phone number or url can’t be random and still function. The 88% difference between proteins among species could indicate 88% different function, not random non-functional changes through common descent.

    The phosphorylation post translational modification is one of several post translational modifications that require specific amino acid sequences to serve as addresses for the phosphorylation site. Eukaryotes have a lot of phosphorylation. Note the difference between Eukaryotes and Prokaryotes.

    It would not surprise me if plants and animals have a different phosphoproteome even for the same proteins.

    https://en.wikipedia.org/wiki/Protein_phosphorylation

    There are thousands of distinct phosphorylation sites in a given cell since:
    1.There are thousands of different kinds of proteins in any particular cell (such as a lymphocyte).
    2.It is estimated that 1/10 to 1/2 of proteins are phosphorylated (in some cellular state).
    3.Independent studies indicate that 30-65% of proteins in the human genome and ~50% of proteins in the yeast genome may be phosphorylated.[9][20]
    4.A statistical analysis of numerous high-throughput and low-throughput experiments estimates that 230,000 156,000 and 40,000 phosphorylation sites exist in human, mouse and yeast, respectively[20]
    5.Phosphorylation often occurs on multiple distinct sites on a given protein.

    Since phosphorylation of any site on a given protein can change the function or localization of that protein, understanding the “state” of a cell requires knowing the phosphorylation state of its proteins. For example, if amino acid Serine-473 (“S473”) in the protein AKT is phosphorylated, AKT is, in general, functionally active as a kinase. If not, it is an inactive kinase.

    Phosphorylation sites are crucial for proteins and their transportation and functions. They are the covalent modification of proteins through reversible phosphorylation. This enables proteins to stay inbound within a cell since the negative phosphorylated site disallows their permeability through the cellular membrane. Protein dephosphorylation allows the cell to replenish phosphates through release of pyrophosphates which saves ATP use in the cell.[21] An example of phosphorylating enzyme is found in E. coli bacteria. It possesses alkaline phosphatase in its periplasmic region of its membrane. The outermost membrane is permeable to phosphorylated molecules however the inner cytoplasmic membrane is impermeable due to large negative charges.[22] In this way, the E. coli bacteria stores proteins and pyrophosphates in its periplasmic membrane until either are needed within the cell.

    Recent advancement in phosphoproteomic identification has resulted in the discoveries of countless phosphorylation sites in proteins. This required an integrative medium for accessible data in which known phosphorylation sites of proteins are organized. A curated database of dbPAF was created, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. The database currently holds 294,370 non-redundant phosphorylation sites of 40,432 proteins.[23] Other tools of phosphorylation prediction in proteins include NetPhos[24] for eukaryotes, NetPhosBac[24] for bacteria and ViralPhos[25] for viruses.

    Serine[edit]

    There are a large variety of serine residues, and the phosphorylation of each residue can lead to different metabolic consequences.
    Protein kinase N1 is responsible for the phosphorylation of the TNF receptor-associated factor (TRAF1) on serine 139 under specific conditions. Murine TRAF1 is also phosphorylated by the same kinase, which leads to the silencing of IKK/NF-κB activity. The elimination of phosphorylation on serine 139 can be achieved by the replacement of TRAF1 with an Alanine residue, which consequently leads to the improved recruitment of TBK1.[26]
    At the serine 789 residue, FGFR1 is phosphorylated by RSK2 when the kinase is in its active form. The signaling capabilities of FGFR1 at the serine 777 site can be weakened by phosphorylation. Serine 1047 and serine 1048 have been linked to the decreased binding affinity of ubiquitin ligase c-Cbl to EFGR when they are phosphorylated.[27]
    When serine 349 is phosphorylated, the binding affinity between protein complex p62 and the protein Keap1 is strengthened, which is linked to stress response.[28]
    When serine 337 is phosphorylated by protein kinase A in vitro, the DNA binding efficiency of the p50 subunit of NF-κB is greatly increased.[29]

    Tyrosine[edit]

    Main article: Tyrosine phosphorylation

    Tyrosine phosphorylation is fast to react and the reaction can be reversed. Being one of the major regulatory mechanisms in signal transduction – cell growth, differentiation, migration and metabolic homeostasis are cellular processes maintained by tyrosine phosphorylation. The function of protein tyrosine kinases and protein-tyrosine phosphatase counterbalances the level of phosphotyrosine on any protein. The malfunctioning of specific chains of protein tyrosine kinases and protein tyrosine phosphatase has been linked to multiple human diseases such as obesity, insulin resistance, and type 2 diabetes mellitus.[30] Phosphorylation on tyrosine doesn’t occur in just eukaryotes but has been discovered to occur in a selection of bacterial species and present among prokaryotes. Phosphorylation on tyrosine maintains the cellular regulation in bacteria similar to its function in eukaryotes.[31]

    Arginine[edit]

    Arginine phosphorylation in many Gram-positive bacteria marks proteins for degradation by a Clp protease.[12]

    Evolution[edit]

    Protein phosphorylation is common among all clades of life, including all animals, plants, fungi, bacteria, and archaea. The origins of protein phosphorylation mechanisms are ancestral and have diverged greatly between different species. In eukaryotes, it is estimated that between 30 – 65% of all proteins may be phosphorylated, with tens or even hundreds of thousands of distinct phosphorylation sites.[32][20] Some phosphorylation sites appear to have evolved as conditional “off” switches, blocking the active site of an enzyme, such as in the prokaryotic metabolic enzyme isocitrate dehydrogenase. However, in the case of proteins that must be phosphorylated to be active, it is less clear how they could have emerged from non-phosphorylated ancestors. It has been shown that a subset of serine phosphosites are often replaced by acidic residues such as aspartate and glutamate between different species. These anionic residues can interact with cationic residues such as lysine and arginine to form salt bridges, stable non-covalent interactions that alter a protein’s structure. These phosphosites often participate in salt bridges, suggesting that some phosphorylation sites evolved as conditional “on” switches for salt bridges, allowing these proteins to adopt an active conformation only in response to a specific signal.[33]

    There are hundreds of known eukaryotic protein kinases, making them one of the largest gene families. Most phosphorylation is carried out by a single superfamily of protein kinases that share a conserved kinase domain. Protein phosphorylation is highly conserved in pathways central to cell survival, such as cell cycle progression relying on Cyclin-dependent kinases (CDKs), but individual phosphorylation sites are often flexible. Targets of CDK phosphorylation often have phosphosites in disordered segments, which are found in non-identical locations even in close species. Conversely, targets of CDK phosphorylation in structurally defined regions are more highly conserved. While CDK activity is critical for cell growth and survival in all eukaryotes, only very few phosphosites show strong conservation of their precise positions. Positioning is likely to be highly important for phosphates that allosterically regulate protein structure, but much more flexible for phosphates that interact with phosphopeptide-binding domains to recruit regulatory proteins.[34]

    Comparisons between eukaryotes and prokaryotes[edit]

    Protein phosphorylation is a reversible post-translational modification of proteins. In eukaryotes, protein phosphorylation functions in cell signaling, gene expression, and differentiation. It is also involved in DNA replication during the cell cycle, and the mechanisms that cope with stress-induced replication blocks. Compared to eukaryotes, prokaryotes use Hanks-type kinases and phosphatases for signal transduction.[35] Whether or not the phosphorylation of proteins in bacteria can also regulate processes like DNA repair or replication still remains unclear.[36]

    Compared to the protein phosphorylation of prokaryotes, the studies done in the protein phosphorylation in eukaryotes of yeast and human cells have been more extensive. It is known that eukaryotes rely on the phosphorylation of the hydroxyl group on the side chains of serine, threonine, and tyrosine. These bases are the main regulatory post-translational modifications in eukaryotic cells but the protein phosphorylation of prokaryotes are less intensely studied. While serine, threonine, and tyrosine are phosphorylated in eukaryotes, histidine and aspartate is phosphorylated in prokaryotes. In bacteria, histidine phosphorylation occurs in the phosphoenolpyruvate-dependent phosphotransferase systems (PTSs), which are involved in the process of internalization as well as the phosphorylation of sugars.[37]

    Protein phosphorylation by protein kinase was first obtained by E. coli and Salmonella typhimurium and has since been demonstrated in many other bacterial cells.[38] It was found that bacteria use histidine and aspartate phosphorylation as a model for bacterial signaling transduction but in the last few years there has been evidence that has shown that serine, threonine, and tyrosine phosphorylation are also present in bacteria. It was shown that bacteria carry kinases and phosphatases similar to that of their eukaryotic equivalent but they have also developed unique kinases and phosphatases not found in eukaryotes.[37]

    So that’s another reason common design is a better explanation for the nested taxonomic hierarchy that common descent via random modification of an ancestral form. The amino acid sequences are optimized per creature.

    NOTE: something can’t be under selection and neutral at the same time, so optimization can’t be compatible with neutral random walks. If something is maintained by selection, it is also resistant to change. So it’s absurd to claim the changes are functional and selected for and neutral and not selected for at the same time. One could postulate function just popped up randomly, but then one is invoking miracles.

  38. Allan Miller,

    There’s a long-running nonsense game on British radio program “I’m Sorry I Haven’t A Clue” (kinda appropriate) called “Mornington Crescent” (the name of a subway stop). There are no real rules, but once in a while someone says “Mornington Cresent” and gets points. That’s how you’re using “Design”. There’s no reason for it, it’s just that when you can’t think of anything to say, say that.

    Funny. I thought I was just engaging in the subject of the op 🙂

  39. colewd,

    Funny. I thought I was just engaging in the subject of the op

    Not in any sensible way. If your answer to every question is ‘Design’, you might as well be saying ‘Mornington Cresent’.

    Why do opposite charges attract? Design. Why is my client’s DNA all over the crime scene? Design. Where did this disease come from? Design. Fun, isn’t it?

  40. So – why did God put the same transposon sequence at a given site in two closely related species of whale? And another in 3 species, including the first two, but not any others? And so on?

  41. From this paper:
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819829/pdf/ieru-12-469.pdf

    Analyzing evolutional conservation
    Studies of the evolutionary conservation of the localization and
    sequence bias of phosphorylated amino acids have yielded conflicting
    results [84]. Phosphorylation sites are generally assumed
    not to be well conserved between species [103], despite the fact
    that phosphorylation site numbers of proteins within signaling
    pathways are similar between species [104].

    Phylogeny proves itself worthless again for molecular biology.

    Analysis of sequence specific features
    The above-described analysis strategies treat phosphorylation
    site changes as if there were changes in gene expression or protein
    abundance. This way of analysis neglects a crucial layer of
    information, which is provided in the phosphorylation sites
    and the surrounding amino acid sequence context.

    The bolded portion refers to the sequence constraints which prevent proteins from evolving willy nilly from one species to another.

    Below is an illustration of short binding motifs on the protein, but note, they don’t include the addressing schemes that would certainly make the sequences that are associated with the binding site much longer.

  42. Rumraket: “The designer deliberately made a nested hiearchy, which is only predicted by evolution”.

    Evolution doesn’t predict a nested hierarchy, and even if it did, it doesn’t predict the one we have.

    But we thank you for your opinion.

  43. Sal persists in posting long, irrelevant quotes and pictures. Bill persists in one-line non sequiturs. When will somebody address the subject of the thread?

  44. stcordova,

    How many sites in a typical protein are under this assumed constraint? I think you’re reaching a bit if you want this to be a general constraint on the entirety of evolution.

    The lack of conservation suggests that there is not even much of a constraint in any case.

  45. Alan Fox: Made me wonder whether hippos have any abilities in underwater communication.

    Further evidence that hippos evolved from whales.

  46. Allan Miller,

    So – why did God put the same transposon sequence at a given site in two closely related species of whale? And another in 3 species, including the first two, but not any others? And so on?

    Whale design is above my pay grade but in the case of macintosh laptops some versions have only silicon memory and some have hard disc memory depending on the tradeoff between total memory, memory cost and footprint.

  47. Allan Miller: Do you seriously think convergence confuses us into thinking whales are closer to bats, because of echolocation?

    Why are you looking at just one character? You can’t look at just one character.

  48. Mung,

    Why are you looking at just one character? You can’t look at just one character.

    Well, yeah. I’ve never argued otherwise, how odd that you’d think I would. I was asking Bill if he seriously thought one convergent feature would fool us in that way.

  49. Allan Miller: So – why did God put the same transposon sequence at a given site in two closely related species of whale? And another in 3 species, including the first two, but not any others?

    Mornington Crescent!

  50. colewd,

    Whale design is above my pay grade but in the case of macintosh laptops some versions have only silicon memory and some have hard disc memory depending on the tradeoff between total memory, memory cost and footprint.

    I think biology is above your pay grade. Transposons are nothing to do with computers.

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