Evolution Easily Refuted

Hi again, Philip:I haven't bothered you for awhile - didn't want you to think everyone was ganging up on you. However, this statement, seems to indicate you've forgotten one of our earlier conversations:

quote:

---

As for speciation going on now please define for the child (and me) just what you're talking about: Irreducible Bacteria? Irreducible species? Perhaps the kid is right? Or will you pull out a definition of speciation that is merely a speculative biological definition of speciation? Perhaps the kid was thinking kinds (e.g., families) whose barriers are more fixed and defy homologous succession(s).

---

I invite your attention to this post and the ones preceeding and subsequent to it, especially your post #50 where you explicitly accept that speciation, using the biological species concept no less, does in fact occur. Have you changed your mind? I am aware you maintain the taxic discontinuity assertion at higher organizational levels (in spite of evidence to the contrary provided, and explanations showing you completely misunderstand what you're arguing against, all of which you've simply ignored), but here you seem to be denying even your original "microevolution is okay" premise.If you're going to blindly cling to your beliefs, at least please be consistent. Otherwise, it's hard to keep track.

quote:

---

Originally posted by Philip:
That's great Taz,

​

You just cleverly argued with a child (high-school perhaps) while handwaving her away with tons of didactic academia.

---

Yeah, I know that many creationists just hate it when they are pushed into the proper definitions of things which they are atempting to debate. Actually I am not sure that you have Dana's age right. I saw that she indicated "student" but she may be anywhere from a highschool student to a grad student. Her writing style could be anywhere inbetween.

quote:

---

Entropy in your stuffy technical definition is oft explained in college science texts by this kid's definition. And entropy appears to manifest our curse empirically enough: i.e., in the thermodynamic decay we see expect to see everywhere and will eventually render our worlds without form and void.

---

First, the text that I used is used in undergrad through grad school, I also provided a more non-tech friendly form for people who are less versed in thermo. Second, the universe is not in a state of "thermodynamic decay" as you said, unless of course you refering to the ever increasing amount "heat energy", which is the least useable form.

quote:

---

As for speciation going on now please define for the child (and me) just what you're talking about: Irreducible Bacteria? Irreducible species? Perhaps the kid is right? Or will you pull out a definition of speciation that is merely a speculative biological definition of speciation? Perhaps the kid was thinking kinds (e.g., families) whose barriers are more fixed and defy homologous succession(s).

---

OK, as you asked a question based in science I am going to use the best available scientific definitions whether you like them or not. A species is a population that is in some way reproductively isolated. THe problem that you seem to have is in understanding that definitions are man made constructs that we use to define real observed phenomina. On the gross scales they are almost 100 % correct, but at the edges they are as grey as the subject matter that they cover (ie geographically isolated species vs species isolated due to mating habits vs species so completely different that they could not mate if they wanted to).

quote:

---

You argue well enough with me, Taz, but you could at least tell the kid you are speculating only, that what you say is not necessarily science, nor Gospel, nor truth; and that what you say really spells: "atheism", "anti-christ", an empirically-trapped awareness, and a pragmatic science at best.

---

And you, Philip, are as arrogant as ever. Nothing that I have said here idicates athiesm or antichrist or anything about god at all. It deals soley with the natural world. What I have described is science, pure and simple. If people in your religious grouping did not act so much to dumb down science it would not BE so hard on people like Dana or even younger students to understand science.

quote:

---

Do you (or anyone out there) really have a mechanism for ANY enzyme (or enzyme family) to have evolved; the thing is impossible. It has never been demonstrated, and never will be, and you and I both know it! The mega-ToE is thus easily refuted. And that is what the child has rightfully asserted.

---

And enzyme does not "evolve" in a natural selection meaning although the common language and sometimes scientific literture will make this error. Living organisms evolve. Now an enzyme can CHANGE through mutation and that change can result ina new activity. I have given you scientific references in the past only to have you blow them off and keep on with your less than impressive "God of Degredation" argument. And the "Child" seems to have learned from people such as yourself who assert in the absence of, or even more importantly in, direct opposition to evidence to the contray of your statements.

quote:

---

Note: You wouldn't try to allude that enzymes be compared to immune-globins, which are exceedingly mysterious, complex, and host-beneficial in their adaptations (as if they were randomly evolving).

---

Please retake a modern immunology course then we will talk. I suggest that you review the somatic cell genetic shuffling that occurs in the immune system.

quote:

---

...Nor would you speculate that enzymes (with their critically aligned active sites) gradually evolved without a god-of-the-gaps heresy.

---

I deal in neither a "god of the gaps" nor in heresy, I will leave these to you.

quote:

---

...Nor that enzymes fell into place like some primordial soup.

---

Again that is a creationist falacy, not mine, therefore I willl leave it to you.

quote:

---

Game over.

---

You're damn right it is, please come back and play when you have game.------------------
"Chance favors the prepared mind." L. Pasteur
Taz[This message has been edited by Dr_Tazimus_maximus, 09-16-2002]

dear Taz,I wondered, are you Dr Max? The one from the Talk-origin site?Best wishes,
Peter

Hi Peter, nope I am afraid not. The nickname Dr. Taz was hung on me by some technicians in a purification cleanroom largely based on the way that I blew through the facility. I do not think that I have ever put anything on the Talk Origins site.------------------
"Chance favors the prepared mind." L. Pasteur
Taz

Welcome Quetzel,I cannot respond at length nor do I wish to concerning Dr. Taz's counter-refutation(s); suffice it to say: the three of us are extremely stubborn in our biases. Nearsighted with regard to trees in the forest...if you will.As always, I appreciate your (Quetzel's) coherent-thought and attention to detail in your refutes; your patiently laying it all down. And yet I became nearsighted with you both (you and Taz) that we might dolefully indulge in some kind of viable mechanism for any enzymes/enzyme-families. I wasn't asking for immune system analogies (a hoax) by Taz; I rebutted them before as inappropriate analogies, period.However your (Quetzel's) reference to the past (on the subject of speciation) still does not explain an enzymatic mega-ToE at all, and you know it, too. All your sophisticated and rhetorical arguments say NOTHING about enzymes; albeit, a convincing piece of NS science.Suffice it to say, with all bigotted arrogance, gentle persuasion, god-of-the-gaps heresies, and/or naturalistic empirical deductive reasoning (your choice)... demonstrate or somehow theorize a micro or mega ToE of enzymes/enzyme families. Then perhaps all this ToE babble will have more substance.Note: If you must succumb to a blind-watchmaker's analogy, at least use terms like 'active sites', 'atomic' and or 'sub-atomic force vectors', 'successive catalytic increments', etc.Take a month or 2 if necessary, especially on that latter mechanism of successive catalytic increments. Until then, enzymatic evolution must remain refuted. Any Voodoo mechanism makes more sense at present.Sincerely,Philip

Hi Philip:I have to confess I understood less of your post than usual. However, it appears that you have jumped on TB's protein family bandwagon. That being the case, since the primary assertion is that the existence of "novel protein families" delineates the taxic discontinuity between "kinds" - thus refuting the ToE - perhaps you can help old TB out with the answer to the question I posed him three times. To wit, please state explicitly which protein families are unique to specific organisms.Try it this way: let's pretend that "kind" is roughly (or at least occasionally) equivalent to the linnean "family" as TB proposes. Please specify which protein families are unique between say, Canidae and Felidae. Note: not specific genes, rather specific families of genes. Or pick a different set for your examples. It doesn't matter. The point is, if you cannot provide at least one single example of completely novel protein families between two related taxa, then your (and TB's) assertion is utter fabrication and god-of-the-gaps handwaving.Take your time.

quote:

---

Originally posted by Quetzal:
Hi Philip:

​

I have to confess I understood less of your post than usual. However, it appears that you have jumped on TB's protein family bandwagon. That being the case, since the primary assertion is that the existence of "novel protein families" delineates the taxic discontinuity between "kinds" - thus refuting the ToE - perhaps you can help old TB out with the answer to the question I posed him three times. To wit, please state explicitly which protein families are unique to specific organisms.

​

Try it this way: let's pretend that "kind" is roughly (or at least occasionally) equivalent to the linnean "family" as TB proposes. Please specify which protein families are unique between say, Canidae and Felidae. Note: not specific genes, rather specific families of genes. Or pick a different set for your examples. It doesn't matter. The point is, if you cannot provide at least one single example of completely novel protein families between two related taxa, then your (and TB's) assertion is utter fabrication and god-of-the-gaps handwaving.

​

Take your time.

---

(...After draining bouts with the flu, Medicare, etc.)
1) Frankly, this arguement (novelity of proteins) doesn't compute on APRIORI grounds.2) I'm speaking of protein-factors, enzymes themselves, not mere protein (aa) sequences, which seem to have nothing to do with my fortuitous-enzyme-formation argument which rebuts the ToE convincingly.3) Of course there is a God-of-the-gaps fallacy when speaking of any form of enzymatic evolution. Atheistic Evo's themselves must succomb to this error like the theistic Evo's; but I'm a YEC who does not require a GOTG explanation.4) TB may respond better to your protein discourse(s); I will re-introduce the ToE-dilemma. How in the world could any enzyme have possibly evolved? Face the music, man (men, women, fellow truth seekers)CONCLUSION:
Knowing full-well that enzymes are fearfully and wonderfully made, why not apply it to your (not you specifically, Quetzel) scientific faith (if there be such a thing).(Here's a side-liner: The 22 or 23 chromosomal pairs found in a human sperm/egg; that this small molecular payload essentially translates to allow for your and my extremely complex existences ... from thousands of pre-birth, birth, childhood phases, puberty, pre-adult, adult phases, etc. These hundreds, thousands, millions, even billions of unique existences that you and I have experienced subjectively and objectively may redemptively go on for some time, Lord-willing.)--Take your time in respondingPhilip

QuetzalThe point about protein families is that they arrive in genomes somehow betwen prokaryotes and mammals. If you don't think there will be protein familes that characterise branches of the tree then I would be very surprised.Will there be genes that characterise each kind? OK, that's more speculative and we need more genomes to test that. But my former statement is accurate and could not be any other way given what we know about protein families.Here's an abstract relevant to the issue showing that about 300(30) genes seperate us from mice (chimps).Finding Genetic Changes of Evolutionary SignificanceMaryellen Ruvolo
Dept. of Anthropology, Harvard University, Cambridge, USAEvolutionarily significant genetic differences between Homo and Pan (i.e.,
those contributing to phenotypic differences) can potentially be of several
forms, given our knowledge of comparative data from other species. These
can range in type from single nucleotide changes in coding or regulatory
regions to the acquisition of novel expressed genes. Although changes in
regulatory evolution are considered to be the primary means by which new
phenotypes are created (Carroll, Grenier, and Weatherbee, 2001), the
acquisition of novel genes is also likely to play a role in Homo-Pan
differences. Given that the human genome has 300 genes which the mouse
genome lacks, this is a net additive gain of 4-5 novel genes per million
years, assuming a 65 million year old common primate-rodent ancestor. If
novel genes were acquired at roughly a constant rate (4-5 genes per million
years per lineage), then we would expect to see approximately 27-28 novel
genes unique to humans since the 6 million year divergence from Pan (and
similarly, the same number of novel genes unique to Pan).New data demonstrate that anthropoid primates have a novel expressed gene,
the chorionic gonadotropin beta-chain gene, not present in the genomes of
other primates or mammals (Maston & Ruvolo, unpublished) which plays a
major role in reproduction and the maintenance of pregnancy. This gene
serves as a model for other newly acquired and expressed genes which are
unique to some primate taxa, similar to those which may distinguish humans
and chimpanzees.PS - how'd that meeting go? Should I bother collecting web-resources etc?[This message has been edited by Tranquility Base, 10-23-2002]

Hi again, Philip. Glad you're feeling better - hope it wasn't anything too serious.

quote:

---

1) Frankly, this arguement (novelity of proteins) doesn't compute on APRIORI grounds.

---

Actually, I agree with you. The argument doesn't compute on ANY grounds.

quote:

---

2) I'm speaking of protein-factors, enzymes themselves, not mere protein (aa) sequences, which seem to have nothing to do with my fortuitous-enzyme-formation argument which rebuts the ToE convincingly.

---

I think you're confused. proteins ARE enzymes, and vice-versa. The terms are synonymous. As far as refuting the ToE, see below.(skipping point 3, which I didn't follow)

quote:

---

4) TB may respond better to your protein discourse(s); I will re-introduce the ToE-dilemma. How in the world could any enzyme have possibly evolved? Face the music, man (men, women, fellow truth seekers)

---

Yep, TB definitely responds better to the protein argument - at least he knows what one is... However, in answer to your "argument from incredulity" question, try this article as representative of literally hundreds of articles on the creation of novel genes (which, after all, mean creation of novel enzymes/proteins): Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL (1998); Selective sweep of a newly evolved sperm-specific gene in Drosophila; Nature 396(6711):572-5

quote:

---

The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.

---

As far as your developmental biology example, feel free to actually derive a genuine argument/point and try again.Thanks for your thoughts. Take care of your flu.

Hi TB:

quote:

---

The point about protein families is that they arrive in genomes somehow betwen prokaryotes and mammals. If you don't think there will be protein familes that characterise branches of the tree then I would be very surprised.

---

Never in a million years (or 6000, whichever comes first ) would I doubt that there will be unique protein families that aren't shared between basal prokaryotes and eukaryotes. I'll even grant that they may each have unique superfamilies. Heck, the two lineages diverged over 2 gya! That's a lot of evolutionary distance. OTOH, the fact that there are gene families that are shared across these two kingdoms means that you can't use the unique ones as your taxic barrier at that level. Unless you've moved the "kinds" to the kingdom level (followed by an awful lot of microevolution), of course.All it takes is for even one gene (not family) to be different followed by 2 billion years or so of divergeance to create wholly unique groups of proteins. However, the question under discussion is the existence of unique protein families as evidence of the unbreachable taxonomic barrier at the linnean family level. So I go back to my original question: please identify the unique protein family that differentiates Felidae from Canidae? It shouldn't require sequencing of the whole genome of all the species within these two families to be able to identify an entire unique protein family (which implies the existence of lots of phylogenetically related genes). Even if it did require such sequencing (and I'll be generous and say "we can't be sure at this time"), this means you CAN'T USE THE ARGUMENT OF THEIR EXISTENCE AS EVIDENCE YOU'RE RIGHT!!!! Until the existence is shown, all you're offering is pure, unbacked speculation. You haven't shown ONE SINGLE UNIQUE FAMILY. C'mon, TB, I'm not asking for much - just that you stop asserting something is true when it's really just the worst kind of baseless speculation.

quote:

---

Will there be genes that characterise each kind? OK, that's more speculative and we need more genomes to test that. But my former statement is accurate and could not be any other way given what we know about protein families.

---

Of COURSE there are going to be unique genes that are different between different taxa! That isn't in dispute at all. I can even show you wildly different genotypes between different populations of the same species, let alone different genera or families. (There are, for example, 24 different karyotypes of freely interbreeding Mus musculus domesticus in the Alps alone! See, for example, Raciation and speciation in house mice from the Alps: the role of chromosomes.) This doesn't help your assertion at all concerning the existence and/or de novo creation of new protein families (don't forget what level you're barking at...).As to the chimp genome article - thanks! It completely refutes your (or maybe it's Philip's) argument that novel proteins can't evolve. Good catch!PS: WRT the meeting. Board "remanded it to a lower court" - i.e., passed the buck to the Bio prof. I sent it directly to her. I expected something more concrete than her "gee, this is great". Like, "I'm gonna use it" or something. So I'd hold off on the references for a bit. No point in jumping through hoops if she's not really going to use the lesson plan. My opinion, it's the best I've seen. Doesn't mean she'll see it the same way. I'll pester her about later in the week and let you know. Again, thanks for your help.[This message has been edited by Quetzal, 10-23-2002]

quote:

---

Originally posted by Quetzal:
I think you're confused. proteins ARE enzymes, and vice-versa. The terms are synonymous.

---

--WOW!
Quetzel, when did enzymes and proteins become one and the same?Dictionary.com plainly states
Enzymes as: "Any of numerous proteins or conjugated proteins produced by living organisms and functioning as biochemical catalysts." Enzymes usually have the suffix '-ase' appended to denote their catalytic functions. Did some Evo twist the definition to make it more credulous?Proteins: "Any of a group of complex organic macromolecules that contain carbon, hydrogen, oxygen, nitrogen, and usually sulfur and are composed of one or more chains of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism."The proteinacious meats we eat? Is some Evo you know calling these enzymes as they sequentially become digested into broken aa chains (raw proteins), urates, and/or fatwa?That is to say, the key word for enzymes: Is it not their active (catalytic) sites? Now we all know that many proteins lack these catalytic sites and thus fail to be synomonous. Fibrils, neurofibrils, myofibrils, albumin ... (most of our flesh) I've never heard referred to as enzymes, albeit some possess varying catalytic effects I grant you. Its exciting to know that such proteins fitly join and have dynamic covalent force vectors and other exquisite force vectors ordering them empirically, and yet which are not catalytic in the purist sense of the word. Else they'd be ICs, too, Quetzel.Your hitchhiker gene mechanism appears suspiciously APRIORI tolerated by, or rather, invoked by more complex enzyme and gene systems of which you and I have a minimal comprehension (i.e., less than 1 percent empirical knowledge).Thank you for your thoughtful reply,Philip[This message has been edited by Philip, 10-23-2002]

QuetzalI hardly see how that abstract demonstrates that genes evolve!Without having seqeunced chimps we have at least one novel gene. The estimate is about 30. You think there wont be unique genes that differentiate cats and dogs? I simply disagree. Mainstream it would be expected using the same extrapolation techniqe outlined in the abstract. (Cats/dogs are seperated by about 40 My mainstream and this would equate to some hundred or so novel genes by extrapolaiton from the man/mouse known genomic novelties).Life-forms are characterizable by the presence of novel enzyme and signalling pathways. New enzymes, that metabolise new classes of non-peptides, have appeared non-stop throughout the supposed evoltuionary sequence. It's not just regulation changes and SNPs.[This message has been edited by Tranquility Base, 10-23-2002]

Uhh, Philip? Reread your definitions. Enzymes are proteins acting as catalysts. Because proteins are pretty ubiquitous, we often change the name to signify their specific actions or use within the organism. For example, contractile proteins are called "muscles" (myofibrils, the bulk of muscle fiber, are composed of the proteins actin and myosin, with a dash of the proteins troponim and tropomyosin for flavor), cell membranes are made of proteins called "collagens" (mostly glycoproteins), "transcription factors" that turn genes on and off are proteins, etc. Back to your basic biology text, there, Philip. The only one twisting definitions is you.Now, would you care to address any of the rest of the post?

Hmm, TB, you're right. I jumped the gun - the abstract doesn't say that. It says anthropoid primates have a novel expressed gene not shared by other primates. No surprises. However, since the abstract ALSO discusses the acquisition rate of novel genes, I'd be willing to bet the full article discusses "how" these novel genes are acquired. Too bad it's unpublished. Since you found the abstract, do you have access to the full article?In any event, this doesn't change the problem you've got about novel protein families, now does it? Single genes don't count - your contention is that whole gene families are acquired de novo (or should that be ex nihilo?) as the taxic barrier between kinds. This has yet to be shown by you.

QuetzalI really think you are assuming what every evolutionist assumes - that people know where these genes came from.They simply don't.The papers on this stuff are far and few between.