Working out a gentleman’s agreement between TSZ and my publishing activities

As much as the TSZ regulars may have sharp disagreement with many of my views, I actually have a vested interest in seeing TSZ survive and prosper and attract participation with talent and brains. TSZ is valuable because of the quality of the participants, namely, professors (like Joe Felsenstein, Jeff Shallit), textbook authors (like Larry Moran), specialists (Tom English, John Harshman, Mark Frank, Mike Elzinga, etc.), academics, practicing scientists, etc. I suspect JohnnyB and VJTorley might have comparable reasons for their participation at TSZ.

The purpose of me posting here is to see what sort of INFORMAL gentleman’s agreement can be worked out to the mutual benefit of TSZ and my publishing efforts.

I’ve slowly and steadily grown a small publishing and reporting business in private creationist venues, but now am expanding to more public venues. The private venues were private primarily because the content was very obscure (like say the 4D nucleome project at the NIH) and of interest to a handful of creationists willing to pay for my reporting to them directly. A quasi private report that will soon become public is my nylonase paper (assuming it gets through all the approval channels for public release).

The main part of the nylonase paper is 15 pages, the supplemental parts are over 60 pages. This has value to the ID and creationist communities because the nylonase topic has been used as an objection to the published work of several ID authors. So, one can see the cultural and potential monetary value of the nylonase project. Part of the financing of the project entailed covering the week of expenses connected to the Lipscomb conference where I got the chance to confer with biochemists and specialists about nylonases among other topics like chromatin and speciation. See:

My presentation at Lipscomb University in front of faculty and deans of several universities available for free online (expense for live attendance is $390)

My participation at TSZ has cleaned up a lot of errors on material that I pass on to the readers of my publications. I get all this free-of-charge editorial review, and that translates into the value of the product I’m marketing to my paid readers. So, that’s the picture from my end.

I want TSZ to thrive and prosper as a community because I believe it is a good thing that these topics can be debated and explored. In contrast to the way Barry Arrington ran UD, I think there is a place for exploration blogs vs. advocacy blogs. UD was an advocacy blog, and TSZ is more an exploration blog. Whereas Barry was eager to demonize and devalue his opponents, I valued my opponents for their ability to correct my misunderstandings and give me lots of free-of-charge tutoring on subjects I was unfamiliar with. Barry really resented my way of doing business….

So my question is:

What is there of value that I can give to TSZ in exchange for the value it has given me? And if not something of value, how can I at least minimize any negative impact I have of TSZ.

Specifically, what is an orderly way of me alerting TSZ of some of the things I’m publishing without simultaneously flooding TSZ with stuff the readers don’t want to read? How can this be done in a way that adds value to TSZ and aligns with TSZ’s vision?

Now granted, many of you would seem quite happy to see creationists go away forever and thus usher in a Darwinist utopia. If that means I don’t participate here, then this is a time to say so. If however you see some value in me maintaining a relationship, please state how you think I can provide value to you. If all I do is provide free entertainment, then that counts for something.

Now, I owe John Harshman a post on common design. So I have some idea about what you guys want to debate me on, and usually stuff I’m not too good at defending and stuff people feel they can publicly trip me up on. Fair enough. I pick some topics I want to talk about, and some topics the TSZ critics want to talk about. Quid pro quo.

What I had in mind is that I post either in my websites or moderately well-trafficked websites like Crev.Info and somehow alert TSZ about something I wrote. I think I can do the alert through sandbox. For a particularly important article, I may create a separate post here at TSZ. However in that case I view that as me requesting a favor of the participants in reading what I have to say, so I will minimize such postings.

PS
This topic also has some relevance on what value the website has to its readers and value to Lizzie’s original vision for TSZ. It is in this larger context that a discussion of what value I can add to TSZ can be discussed. But I think a conversation or at least some thought might be explored as to why people participate here and why and how the website should continue.

PPS
some sample threads I’ve started:

When did nylon-eating proteins actually evolve the ability to eat nylon?

Barry Arrington’s Bullying

For VJ Torley: Christianity’s consistency with Evolutionary Theory, JB Peterson’s Interview

In Slight Defense of Granville Sewell: A. Lehninger, Larry Moran, L. Boltzmann

My presentation at Lipscomb University in front of faculty and deans of several universities available for free online (expense for live attendance is $390)

Reflections of a Former Missionary

PPPS
Fwiw there is now TheSkepticalZone.Wordpress.Com website. I give it to the admins here as a present to do what they wish with it.

Many thanks to Alan Fox and Neil hosting my comments and threads here at TSZ.

117 thoughts on “Working out a gentleman’s agreement between TSZ and my publishing activities

  1. stcordova: Not if the group can’t naturally arise from descent with modification naturally.Therefore it’s an assumption that one group naturally arose from another when it wasn’t confirmed that it was actually naturally possible.

    I think you don’t understand what “naturally” was doing in that sentence, and that makes everything you say here both unnecessary and irrelevant. It’s a common creationist blind spot: confusing common descent with the cause of change. Somehow they just can’t imagine that common descent is implied by nested hierarchy even if god personally poofed every mutation into existence. Because if he did that, he still did it in the context of a phylogenetic tree: particular mutations in particular spots on the tree.

    Once again: the question of whether particular transformations are possible through known mechanisms (which is what you presumably mean by “naturally”) is irrelevant to the question of whether the pattern of transformations is evidence of common descent.

    What I meant by “naturally” is that nested hierarchy is the obvious result of common descent; if there is common descent we expect to see nested hierarchy. Do you disagree?

    Now that may seem ironic since it seems I want to obliterate belief in evolution from as many peoples lives that I can on planet Earth.But I believe quality dialogue is one way to achieve that end.

    Yeah, you’re wrong about that. Cherry-picking and ignoring most of the data is what you need. But we’ll see.

    The good stuff I develop in dialogue here I pass on to my paid customers.I might not eliminate belief in evolution from anyone here at TSZ, but debate here helps me refine my arguments for consumption by my customer base.I have a policy of passing on only what my conscience deems credible. I could be wrong, but it is passed on in good faith.

    This disturbs me a bit. I think you will have a filter for what you pass on. Even if that filter is unconscious, and I will be charitable and assume it is, you have as much as said that your conclusion is foregone. You will pass on only arguments that you think will show what you want to show. On some level, that’s less than honest.

  2. This disturbs me a bit. I think you will have a filter for what you pass on. Even if that filter is unconscious, and I will be charitable and assume it is, you have as much as said that your conclusion is foregone. You will pass on only arguments that you think will show what you want to show. On some level, that’s less than honest.

    For the record, to ensure paid customers have access to opposing views, I was thinking of referring them to discussion at TSZ or some repository. The one-day old idea of TSZ-2 was part of a that, but I canned the idea in deference to what you and Keiths feedback. I want to maintain what little good will can be maintained between opposing sides, and I expressed commitment to supporting the progress of this site.

    I own the domain, DebateEvolution.com

    I’m considering inviting commentary there. I haven’t figured out how to filter dumb commentary from expert commentary.

    For example, if some chemist like Larry Moran said, “Sal, your diagram is ok, but represent the nylon molecule in the ionized state.” I would take that into serious consideration. If he said, “your paper sucks.” Well, people will have access to it. The voice won’t be suppressed. But it won’t change my mind.

    One customer did, quite by accident see my post at TSZ on Alus through google. He thought I was polemic, but on the whole correct. I actually was vindicated in light of the fact biochmeistry textbooks echo what I claimed. So this was the thread:

    http://theskepticalzone.com/wp/some-evidence-alus-and-sines-arent-junk-and-garbologists-are-wrong/

    Compare what I said in the comment section with Lehniger 2016, a rival biochem textbook to Moran’s:

    The ADAR-promoted A-to-I editing is particularly common in transcripts derived from the genes of primates. Perhaps 90% or more of the editing occurs in Alu elements, a subset of the eukaryotic transposons called short interspersed elements (SINEs), that are particularly common in mammalian genomes. There are over a million of the 300 bp Alu elements in human DNA, making up about 10% of the genome. These are concentrated near protein-encoding genes, often appearing in introns and untranslated regions at the 3′ and 5′ ends of transcripts. When it is first synthesized (prior to processing), the average human mRNA includes 10 to 20 Alu elements. The ADAR enzymes bind to and promote A-to-I editing only in duplex regions of RNA. The abundant Alu elements offer many opportunities for intramolecular base pairing within the transcripts, providing the duplex targets required by the ADARs. Some of the editing affects the coding sequences of genes. Defects in ADAR function have been associated with a variety of human neurological conditions, including amyotrophic lateral sclerosis (ALS), epilepsy, and major depression.

    The genomes of all vertebrates are replete with SINEs, but many different types of SINES are present in most of these organisms. The Alu elements predominate only in the primates. Careful screening of genes and transcripts indicates that A-to-I editing is 30 to 40 times more prevalent in humans than in mice, largely due to the presence of many Alu elements. Large-scale A-to-I editing and an increased level of alternative splicing (see Fig. 26–21) are two features that set primate genomes apart from those of other mammals. It is not yet clear whether these reactions are incidental or whether they played key roles in the evolution of primates and, ultimately, humans.

    Nelson, David L.; Cox, Michael M.. Lehninger Principles of Biochemistry (Page 1113). W.H. Freeman. Kindle Edition.

    I delivered quality and accuracy in that discussion which is more than I can say for DNA_jock.

    You see the exchange in that thread, and who would they think is more credible in light of that passage in Lehningher (which by the way I found during one of my visits to the NIH).

    DNA_jock could piss all over what I had to say, but he’s effectively pissing over the latest and greatest textbook biochemistry.

  3. Sal,

    Keiths apparently lives in an alternate reality of his own making. He provided lots of entertainment for me when he couldn’t even solve a question on a college exam regarding the entropy change of an ice cube with is approach. Too funny.

    First of all, those who know you know better than to take your self-serving descriptions at face value.

    Second, that episode is actually a nice example of a face-saving scordova evasion.

    I presented you with a list of objections showing that the energy dispersal view of entropy, which you had embraced, could not be correct. Instead of responding to my objections, which were fatal to your position, you kept asking me to solve an irrelevant problem which was in no way fatal to mine.

    That you would try to spin that as a victory is laughable. But very scordovan.

  4. stcordova,

    Sal, where can we get more information on your amazing, and fittingly heartless Darwinian, tax plan?

    I would be fascinated to read about it, if you do a paper on it.

  5. Keiths:

    First of all, those who know you know better than to take your self-serving descriptions at face value.

    Second, that episode is actually a nice example of a face-saving scordova evasion.

    Tell the readers how much graduate level statistcal mechanics and thermodyanimics you studied. My classmates in those classes would find your opining hilarious.

    Here is an example I posed to Keiths which he couldn’t solve using his approach to thermodynamics:

    http://theskepticalzone.com/wp/in-slight-defense-of-granville-sewell-a-lehninger-larry-moran-l-boltzmann/comment-page-8/#comment-145795

    problem from a Chemistry exam at Simon Frasier University in Canda.

    http://www.sfu.ca/~mxchen/phys3441121/Mt1Solution.pdf

    QUESTION:

    We have a 20 g cube of ice at 273 Kelvin (melting temperature). The latent heat of melting is 333 grams/Joule. What is the entropy change (neglecting the slight change in volume from solid to liquid phase).

    SOLUTION:

    T = 273 K

    Hmm, so how much energy is dispersed from the surroundings into the ice cube?

    Delta-q = Energy crossing thermodynamic barrier between environment and ice cube.

    delta-q = 333 grams x 20 J/ gram = 6660 Joules

    What is the entropy change. Since the process is isothermal, the Clausius integral evaluates trivially to:

    delta-S = delta-q / T = 6660 J /273 K = 24.4 J/K

    So 6660 Joules of energy gets dispersed from the environment into the ice cube. We just have to scale it down by the temperature to get the quantitative change in entropy of 24.4 J/K.

    So the energy dispersal description works in understanding entropy.

    Now Keiths can answer this simple college level chem question using his observer-dependent ignorance measurements and also not reference the energy dispersal of 6660 J going into the ice cube since he says energy dispersal is a misconception.

    He needs to show his work too.

    He couldn’t of course solve the problem with his “entropy is observer ignorance” approach, because, well he’s Keiths. 🙂

    And that is why, after Keiths stopped being entertaining and could not even pitch the baseball into the strike zone for my batting practice, he got demoted to my ignore list most of the time. Same with phoodoo.

    Speaking of which, was that you Keiths who figured out how to activate the ignore list at TSZ? Thanks your a pal. For that, you are hearby promoted to the status of Friend of Sal (FOS).

  6. stcordova: Here is an example I posed to Keiths which he couldn’t solve using his approach to thermodynamics:

    Out of interest, can you calculate the amount of heating from friction that would be generated if it rained enough to cover the all the worlds mountains?

  7. stcordova:
    And that is why, after Keiths stopped being entertaining and could not even pitch the baseball into the strike zone for my batting practice, he got demoted to my ignore list most of the time.

    Yet:

    stcordova: . The one-day old idea of TSZ-2 was part of a that, but I canned the idea in deference to what you and Keiths feedback.

  8. J-Mac: There are more than one OEC ideas but none of them fits the data of 13.7 billion old earth as far as I know

    I agree with that one. There are no 13.7 billion year old Earth-models that fi the data. lol

  9. OMAgain:

    Yet:

    I said Keiths is on my ignore list most of the time. Do you not understand that “most” is not the same as “all”? I’m looking at comments from people I usually ignore because I have extended an invitation for feedback.

    Hope that clarifies if for you, pumpkin.

  10. stcordova: Hierarchically arranged similarities exist independent of the assumption of common descent. You don’t need the assumption of common descent to see hierarchically arranged similarities. Common descent is a gratuitous and superflouous add on. Creationists since Linnaues saw hierarchy in biology!

    And here we see that you don’t actually understand the evidence for common descent.

    It is the multiple nesting hierarchies, the fact that different data sets converge on the same overall tree structure, that implies common descent.

    If the trees you got from different core genes gave wildly different trees, common descent would be falsified. But there is only one theory that predicts the trees constructed from independent data sets to be highly congruent: Common descent.

  11. I like TSZ’s ability to record all comments and then provide an ignore mechanism.

    I would like a means of higher tier commenters (like University professors or professional researchers with expertise in relevant fields) posting their objections and criticisms so I am made aware of them and that they are highlighted and eventually addressed.

    This will be of interest regarding the nylonase paper.

    I’m tempted to direct critical commentary to threads at TSZ specifically about my nylonase paper.

    I suspect the Discovery Institute will promote the paper if they are convinced it holds up since it would help discredit critics of DI authors like Stephen Meyer and Bill Dembski who were subject to Ken Miller using the nylonase argument against them.

    A DI or Biocomplexity staff member did indirectly invite me through the Blyth Institute to write something else for them, but I haven’t gotten around to it since I was so busy with the nylonase project.

  12. Basically what Sal is saying is that he wants a free portal to advertise himself, with functions that help in that endeavor.

    More handouts for Sal.

  13. And here we see that you don’t actually understand the evidence for common descent.

    It is the multiple nesting hierarchies, the fact that different data sets converge on the same overall tree structure, that implies common descent.

    Common descent would create hierarchies with qualification. There is a lack of INTRA-species and INTRA-group (as in the same group) variation. It’s hard for me to explain this now, but I’ve alluded to it here and there. I’m taking the advanced bioinformatics class hoping I can improve and articulate the problem.

    I alluded to the problem regarding aminoacyl-tRNA-synthetases (aaRS) genes. The e-coli genes and groups of other bacteria have too little INTRA species and INTRA group variation. No one except me seems interested in this, just like I and one other person on the planet was interested in the angle I took on the nylonase paper.

    So, one step at a time. I need to do well on the nylonase paper, and then build from that. Part of doing well on the nylonase paper is subjecting it to open access public criticism and correction. I think I’m right, but I can always improve the way I present my arguments, and I’m sure I have a few minor corrections that I have not yet seen.

    But back to common descent. One can assume it happened, but it doesn’t mean it doesn’t require miracles to make it work. It’s just an assumption the transitions from one form to another are feasible and ordinary and bridgeable by ordinary mechanism working for millions of years. That’s an assumption, it’s not proven, and not believable for several cases I’ve thought of.

    I mentioned chromatin evolution as a barrier. How about the evolution of specialized neurons. How about specialized topoisomerases? The list is endless…

  14. phoodoo: Rumraket: wildly

    Do you have a definition for wildly? Is that word measurable?

    What if the trees are just different, would that suffice?

    Phoodoo, in the other thread where you and I had an exchange on this exact subject, I gave you links to the relevant literature. Yes, there is an objective measure of the degree to which independent data sets diverge enough to contradict common descent.

    So here it is again, from Theobald’s 29+ Evidences for macroevolution. http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence:

    In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are “When comparing two measurements, how much of a discrepancy does it take to be a problem?” and “How close must the measurements be in order to give a strong confirmation?” Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).
    (…)
    When two independently determined trees mismatch by some branches, they are called “incongruent”. In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see “Statistics of Incongruent Phylogenetic Trees”.

    The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

    “Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106.” (Penny and Hendy 1986, p. 414)

    Note the references to things like statistical significance.

    In fact, do yourself a favor and read this whole section: http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy

    Prediction 1.2: A nested hierarchy of species

    As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as “groups within groups”, otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics.

    The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of “the great chain of being” and the continuums predicted by Lamarck’s theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

    There is more, read the whole thing, particularly the section on Consistency Index also.

    If it were impossible, or very problematic, to place species in an objective nested classification scheme (as it is for the car, chair, book, atomic element, and elementary particle examples mentioned above), macroevolution would be effectively disproven. More precisely, if the phylogenetic tree of all life gave statistically significant low values of phylogenetic signal (hierarchical structure), common descent would be resolutely falsified.

    In fact, it is possible to have a “reciprocal” pattern from nested hierarchies. Mathematically, a nested hierarchy is the result of specific correlations between certain characters of organisms. When evolutionary rates are fast, characters become randomly distributed with respect to one another, and the correlations are weakened. However, the characters can also be anti-correlated—it is possible for them to be correlated in the opposite direction from what produces nested hierarchies (Archie 1989; Faith and Cranston 1991; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991). The observation of such an anti-correlated pattern would be a strong falsification of common descent, regardless of evolutionary rates.

    One widely used measure of cladistic hierarchical structure is the consistency index (CI). The statistical properties of the CI measure were investigated in a frequently cited paper by Klassen et al. (Klassen et al. 1991; see Figure 1.2.1). The exact CI value is dependent upon the number of taxa in the phylogenetic tree under consideration. In this paper, the authors calculated what values of CI were statistically significant for various numbers of taxa. Higher values of CI indicate a greater degree of hierarchical structure.

    As an example, a CI of 0.2 is expected from random data for 20 taxa. A value of 0.3 is, however, highly statistically significant. Most interesting for the present point is the fact that a CI of 0.1 for 20 taxa is also highly statistically significant, but it is too low—it is indicative of anti-cladistic structure. Klassen et al. took 75 CI values from published cladograms in 1989 (combined from three papers) and noted how they fared in terms of statistical significance. The cladograms used from 5 to 49 different taxa (i.e. different species). Three of the 75 cladograms fell within the 95% confidence limits for random data, which means that they were indistinguishable from random data. All the rest exhibited highly statistically significant values of CI. None exhibited significant low values; none displayed an anti-correlated, anti-hierarchical pattern.

    These are things creationists and ID proponents generally stay away from, because they have no answer to and don’t even know how to begin to address. To be fair, I wouldn’t know how to do that work either, but I’m not the idiot claiming all the experts who do the kind of work required to assess the validity of CI scores, are wrong.

    IDcreationists like to speak colloquially about some handpicked examples. like Sal does above (just make a number of bold claims, but don’t actually demonstrate the truth of them using the proper methods and subjecting them to real peer review by qualified experts).

  15. stcordova: I mentioned chromatin evolution as a barrier. How about the evolution of specialized neurons. How about specialized topoisomerases? The list is endless…

    Wow, you mentioned it is an evolution barrier? That’s just great. Then I can mention that it isn’t. If you just mentioning something as an evolution barrier, makes it an evolution barrier, the me mentioning it isn’t, means it isn’t. If it works for you, it works for me.

    But let’s not kid ourselves here of course. Things don’t become true just because we say the words. I doubt you’ve done the actual work to show chromatin can’t evolve, I think that’s just something you believe.

    Can you explain why it would be an evolution barrier, instead of just mentioning (aka merely asserting) it is?

    Why can’t chromatin evolve? Show your work. As in show with logical arguments and mathematical calculations, that chromatin couldn’t evolve. Your hunches are worth nothing. Do the actual work.

  16. Rumraket,

    Yes, Rumraket, but that is sort of the whole weakness of the evolution fairytale. You can say anything is possible, without saying how or why. Then just say, prove it can’t!

    Well, prove there is no God.

  17. phoodoo:
    Basically what Sal is saying is that he wants a free portal to advertise himself, with functions that help in that endeavor.

    More handouts for Sal.

    Sal has picked out a niche in which he succeeds , evolution in action

  18. phoodoo:
    Rumraket,

    Yes, Rumraket, but that is sort of the whole weakness of the evolution fairytale.You can say anything is possible, without saying how or why.Then just say, prove it can’t!

    Well, prove there is no God.

    If there’s evidence that two species, one with and one without chromatin, share a common ancestor, that counts as evidence for how (descent with modification) and why (the phylogenetic evidence) it’s possible

    I’m sure even you can understand that simple fact

  19. phoodoo: I can’t find the definition of “wildly” anywhere in there. Perhaps I missed it.

    When I used the word wildly I was just speaking colloquially. The correct term is statistically significant. It is telling you want to focus on the specific word, instead of the article quoted that explain the concepts.

  20. phoodoo:
    Rumraket,

    Yes, Rumraket, but that is sort of the whole weakness of the evolution fairytale.You can say anything is possible, without saying how or why.

    No, you can’t.

    But when someone says some biological entity can’t possibly evolve, they’re making a claim and must support it. Any claim for evolution has a burden of proof, but so does a claim against it.

    Why? Let’s put aside evolution, look at astronomy instead. There’s some theory of nuclear fusion that takes place in stars. One of them is called the CNO-cycle. Carbon-Nitrogen-Oxygen cycle. It’s a theory that describes a nuclear fusion process by which the elements C, N, and O are part of a process by which helium is produced in stars. That’s a theory, and it explains some observations from astronomy. We haven’t ever actually recreated the CNO-cycle experimentally here on Earth (only small aspects of it has been observed). But it’s a nice predictive model, it fits very well with our understanding of how stars, and nuclear physics, work.

    Now someone comes along and says “helium can’t be produced by the CNO cycle”. (that would be analogous to Sal coming along and saying “evolution can’t produce chromatin”).

    So what do we do now, phoodoo? Do we just discard half a century of astronomy and nuclear physics? Or does the person claiming helium can’t be produced through the CNO cycle need to support his claim? Is his mere hunch enough to throw away the models we have that work well in astronomy and nuclear physics?

  21. stcordova: For the record, to ensure paid customers have access to opposing views, I was thinking of referring them to discussion at TSZ or some repository.

    Hardly sufficient, and it doesn’t answer the charge of cherry-picking to fit a foregone conclusion. Failure to confront the big picture is, at bottom, a moral failure.

  22. stcordova: Common descent would create hierarchies with qualification. There is a lack of INTRA-species and INTRA-group (as in the same group) variation. It’s hard for me to explain this now, but I’ve alluded to it here and there. I’m taking the advanced bioinformatics class hoping I can improve and articulate the problem.

    I don’t see how a class could help you articulate what is now completely opaque. Please try, now, to explain what that meant, rather than just alluding to a problem that nobody else can see.

    But back to common descent. One can assume it happened, but it doesn’t mean it doesn’t require miracles to make it work. It’s just an assumption the transitions from one form to another are feasible and ordinary and bridgeable by ordinary mechanism working for millions of years. That’s an assumption, it’s not proven, and not believable for several cases I’ve thought of.

    Do you even read what other people write? Common descent is not an assumption. Is it necessary to put this in all caps? Bold? What could possibly work?

    And another: common descent does not rely on a particular cause of transitions. If you want to believe that every transition is lovingly hand-crafted by an artisanal deity, feel free, as the cause of transitions is irrelevant to the inference of descent. That’s a separate question, best discussed separately. And in fact, having inferred common descent, we can use the resulting trees to investigate causal hypotheses.

    This is what I mean by cherry-picking. You engage with the data and arguments of your opponents only in those rare cases where you think you have an advantage. You ignore everything else.

  23. Do you even read what other people write?

    Yes. It may seem I ignore it because I don’t agree nor do I think you’re correct. So, to be clear, I could just say, “professional phylogeneticist John Harshman insists common descent isn’t an assumption but rather a conclusion. I disagree and say it not only an assumption but an unnecessary add on that doesn’t fit the criteria of mechanical feasibility so it cannot be a conclusion unless non-sequitur conclusions count as conclusions or if speculative ideas count as actual facts.”

  24. stcordova: Yes.It may seem I ignore it because I don’t agree nor do I think you’re correct.So, to be clear, I could just say,“professional phylogeneticist John Harshman insists common descent isn’t an assumption but rather a conclusion.I disagree and say it not only an assumption but an unnecessary add on that doesn’t fit the criteria of mechanical feasibility so it cannot be a conclusion unless non-sequitur conclusions count as conclusions or if speculative ideas count as actual facts.”

    Perhaps if you began to back up your many assumptions about others and their “assumptions,” you might learn to engage the facts.

    The made-up “reality” of IDists/creationists is required in order to leap to the unsupported assertions invented to demonize evolutionary theory and those who accept the evidence.

    Accepting common descent is to a large degree just the recognition that the apparent derivative order of taxonomy that seems to be due to inheritance in fact is due to inheritance. Even several classic taxonomic terms suggest actual relatedness, like “genus,” “family,” and “phylum.” Of course it was recognized that life appears related before it was accepted as truly being related, but the hierarchies were recognized early on as being suggestive of common descent with variation. Evolutionary theories were rather common before Darwin because life simply appears evolved* (and not designed like any actual manner we’ve observed), and the pretense that common descent is an assumption ignores considerable historical evidence to the contrary.

    Glen Davidson

    *The bullshit excuse is that they hated religion, which conveniently bypasses the fact that it was the appearance of life’s derivation that was the great fact needing explanation.

  25. stcordova: Yes.It may seem I ignore it because I don’t agree nor do I think you’re correct.So, to be clear, I could just say,“professional phylogeneticist John Harshman insists common descent isn’t an assumption but rather a conclusion.I disagree and say it not only an assumption but an unnecessary add on that doesn’t fit the criteria of mechanical feasibility so it cannot be a conclusion unless non-sequitur conclusions count as conclusions or if speculative ideas count as actual facts.”

    No, it seems like you ignore it because you ignore it. You have never addressed the question, including in that comment. You ignored my argument, merely repeating your claims. Is it possible that you don’t realize you’re doing it? I won’t repeat my argument; it’s still there, waiting for you to read and respond.

  26. This is John’s argument:

    As Glen said, common descent isn’t a necessary assumption in order to find hierarchy, but it’s the unavoidable conclusion. Your alternative of “common design” is vacuous. There is no reason to expect common design to have such a pattern.

    You want me to respond to it. Responding doesn’t mean agreeing. I respond by saying I don’t find it an unavoidable conclusion, I don’t find common design vacuous, and I think it’s irrelevant what we should or should not expect out of a Designer since it’s not our designs but God’s. That’s my opinion and you are free to view my opinion as non-credible, stupid, whatever. I respect that. But I’ve expressed why I find it hard to change my opinion.

    The problem with me and other creationists believing in common descent is what we view as the unproven assumption it’s feasible for something like a lungfish to eventually have a descendants like Elephants and Birds. I used to be an evolutionist, thought it was a cool theory, thought it was so cool in that scene in movie 2001 where the apes evolved. I just don’t find it believable anymore and think God working a miracle in the recent past is more believable.

    Maybe I’m wrong, but evolutionists haven’t given me (an ex-evolutionist) to change back my mind, and that echoes how other ex-evolutionists like my friend Caroline Crocker a professor of biology dismissed from my undergrad alma mater, George Mason. The same can be said of paleontologist Gunter Bechley or evolutionary biologist Richard Sternberg. And last but not least, John Sanford at Cornell.

    You want to argue our opinion isn’t credible, fine. I respect that. But nothing you’ve said I find convincing. In contrast I find electro magnetic theory and quantum mechanics and relativity convincing and was willing to suffer through a lot of study to learn these theories.

    In contrast, I don’t find the theory of universal common ancestry convincing unless one wants to invoke miracles to make it mechanically feasible, but if one invokes miracles, then one may as well be a creationist.

    You want to label my opinion as lacking credibility, logic, science, etc. That’s fine, and I take no offense. But it’s not completely fair to say I ignored what you said, I just don’t find it convincing. Maybe you can find another creationist that can be more easily converted to your viewpoint than I.

    Sorry to be so difficult, but well, I think you know what to expect from me. Nothing personal. And at some level, I’m sorry we have to disagree, you seem like someone I’d like to get along with.

  27. stcordova: DNA_jock could piss all over what I had to say, but he’s effectively pissing over the latest and greatest textbook biochemistry.

    Please stop that DNA_Jock.

  28. stcordova: In contrast, I don’t find the theory of universal common ancestry convincing unless one wants to invoke miracles to make it mechanically feasible, but if one invokes miracles, then one may as well be a creationist.

    Or anything else.

    What does it matter when you’re just making it up?*

    Glen Davidson

    *Or someone else is.

  29. stcordova:
    This is John’s argument:

    Nope, that wasn’t it, or only part of it. This is the direct response to your claim:
    “And another: common descent does not rely on a particular cause of transitions. If you want to believe that every transition is lovingly hand-crafted by an artisanal deity, feel free, as the cause of transitions is irrelevant to the inference of descent. That’s a separate question, best discussed separately. And in fact, having inferred common descent, we can use the resulting trees to investigate causal hypotheses.”

    You didn’t respond. A response is not just contradiction.

    The problem with me and other creationists believing in common descent is what we view as the unproven assumption it’s feasible for something like a lungfish to eventually have a descendants like Elephants and Birds.

    Ignoring the misunderstanding that lungfish are tetrapod ancestors, why would it not be feasible? I suspect you are alluding to the plausibility of transformation by natural causes. But that once more ignores my point in quotes above.

    I just don’t find it believable anymore and think God working a miracle in the recent past is more believable.

    Why? And what sort of miracle are you talking about? Is that fiat creation of all the fossil and living species in a single week, or is it something else?

    Maybe I’m wrong, but evolutionists haven’t given me (an ex-evolutionist) to change back my mind, and that echoes how other ex-evolutionists like my friend Caroline Crocker a professor of biology dismissed from my undergrad alma mater, George Mason.The same can be said of paleontologist Gunter Bechley or evolutionary biologist Richard Sternberg.And last but not least, John Sanford at Cornell.

    Do you think name-dropping helps you make a case? If not, what’s the point? And yes, you are wrong. I think the fact that you shy away from confronting the main objections to your ideas is evidence that you’re not quite the impartial student of nature you think you are.

    You want to argue our opinion isn’t credible, fine.I respect that.But nothing you’ve said I find convincing.In contrast I find electro magnetic theory and quantum mechanics and relativity convincing and was willing to suffer through a lot of study to learn these theories.

    Might I suggest that’s because those theories don’t threaten your world view?

    In contrast, I don’t find the theory of universal common ancestry convincing unless one wants to invoke miracles to make it mechanically feasible, but if one invokes miracles, then one may as well be a creationist.

    Why? Are you really unable to separate theory X from theory Y and unable to separate the evidence for theory X from the evidence for theory Y?

    But it’s not completely fair to say I ignored what you said, I just don’t find it convincing.

    And yet you ignored what I said, as you ignore most of biology and geology.

  30. John, to Sal:

    I think the fact that you shy away from confronting the main objections to your ideas is evidence that you’re not quite the impartial student of nature you think you are.

    People notice your evasiveness, Sal. It’s a real problem.

    How do you think your subscribers — who actually pay money to you — would feel if they saw how you regularly run away from people who raise objections that you cannot answer?

    By all means, encourage them to read TSZ.

  31. John, to Sal:

    Hardly sufficient, and it doesn’t answer the charge of cherry-picking to fit a foregone conclusion. Failure to confront the big picture is, at bottom, a moral failure.

    Particularly when Sal is literally selling that foregone conclusion, and the cherry-picked “evidence” for it, to his hapless subscribers.

    Shameful.

  32. Glen:

    The bullshit excuse is that they hated religion, which conveniently bypasses the fact that it was the appearance of life’s derivation that was the great fact needing explanation.

    It’s always fascinated me that IDers and creationists seem to hate theistic evolutionists even more than they hate atheistic evolutionists.

    The TEs deprive them of the “it’s only because you hate religion” rationalization.

  33. keiths: How do you think your subscribers — who actually pay money to you — would feel if they saw how you regularly run away from people who raise objections that you cannot answer?

    I presume that’s what they’re paying him for: material to convince them that what they already believe is true along with insulation from unwelcome facts.

  34. I’m confused. You can do what you want, but I doubt people will follow you to other venues for debate. UD and other sites offer lessons on that.

  35. I hope TSZ survives at least until I have the opportunity to publish most of my Mysteries of Evolution…
    I also have a few ideas for OPs on the quantum creation of the universe, consciousness, afterlife, soul, hell, limbo, purgatory, prevalence of evil, omnipotence, omniscience, infinity and so on…over 30 ideas so far… 😉

  36. dazz,

    Thanks. How is the age of the earth dated exactly? Since the earth got formed into a sphere? Since water appeared on it? oxygen etc?

  37. J-Mac:

    What is it now? 4 billion???

    dazz:

    0.0045 billion years in Spain

    Uh-oh. That’s gonna confuse him.

    No, J-Mac, he isn’t saying that Spain is younger than the rest of the planet.

  38. dazz,

    Actually, this theme is included in one of my upcoming OPs on the big bang and the age of the universe…A clue: since the universe doesn’t appear to have a center, how do we know where the beginning of it is?

  39. keiths:
    J-Mac:

    dazz:

    Uh-oh.That’s gonna confuse him.

    No, J-Mac, he isn’t saying that Spain is younger than the rest of the planet.

    Thanks keiths! Your anger motivated sarcasm has been noted…

    BTW: Studies show that anger significantly shortens life expectancy…so you are not going to see any retaliation from me… 😉

    Peace and love!

  40. J-Mac:

    A clue: since the universe doesn’t appear to have a center, how do we know where the beginning of it is?

    That’s not a clue. It’s clueless.

  41. J-Mac:
    dazz,

    Actually, this theme is included in one of my upcoming OPs on the big bang and the age of the universe…A clue: since the universe doesn’t appear to have a center, how do we know where the beginning of it is?

    everywhere is the “center” of the universe

  42. keiths,

    I knew you’d like that one…I guess you are going to have to wait for the actual OP to see what I meant…

    BTW: Don’t blow to much steam! It could be unhealthy…lol

    (See my previous comment )

    Peace and love! 😉

  43. dazz: everywhere is the “center” of the universe

    What? Do you know this for a fact? Or are you just trying to get keiths going?

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