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Author Topic:   Evolving New Information
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 256 of 458 (521956)
08-30-2009 8:30 PM
Reply to: Message 253 by traderdrew
08-30-2009 1:00 PM


traderdrew responds to me:

quote:
Proteins have specific complex shapes and their overall structures are not assembled or conform to standard Euclidean mathematics.

"Geometry." The word you are looking for is "geometry."

And where is your evidence that protein folding is non-Euclidean? Do you even know what that word means? Are you saying in the world of a protein molecule, there is something up with the parallel postulate?

quote:
Common sense says throwing the amino acids together randomly is highly unlikely to generate functional coherence.

And since when is chemistry "random"? When I take two moles of hydrogen gas and a mole of oxygen gas, mix them at STP, and spark the mixture, why is it that the most dominant compound that results is water and not hydrogen peroxide?

As we're finding out by the examination of space, organic molecules are outrageously abundant. You can't get away from them.

But even if we go along with your highly unjustifiable premise that chemical reactions happen in a "random" method, you are ignoring the sheer vastness of the universe.

Let's test your math: Suppose I have darts and a dartboard. For the sake of this experiment, the probability of me hitting the dartboard is inversely proportional to the number of darts I have to begin with. That is, if I have n darts, then each dart has only a 1/n chance of hitting the dartboard.

As the number of darts increases, the chances of hitting the dartboard with any given dart become quite small. Indeed, as the number of darts approaches infinity, the chance of hitting the dartboard with any given dart approaches 0.

But suppose I throw them all. Given an infinite number of darts, each with an infinitesimal chance of hitting the dartboard, what is the probability that I have hit the dartboard at least once?

Given a universe as large as it is, as packed to the brim with organic molecules as it is, where does this idea come from that it is extremely unlikely to have happened? Quite the opposite is true.

quote:
How many articles do proponents of ID need?

Well, currently they don't have any. I think the first goal is to get one. For once they manage to get that first one, other scientists can get to work in examining it, seeing how the results might relate to other phenomena, and develop a coherent theory about what ID actually does.

But so far, there hasn't been a single paper produced that has ever survived review.

quote:
There is also the subject of resistance or pressure organizations may apply against articles that support ID.

Oh...I see. It's a grand conspiracy. Nevermind that overturning the dominant paradigm of a field would win you the Nobel Prize and have every university and laboratory in the world come banging on your door begging you to join their staff. No, the world of science of full of evil atheists who have a deep-seated, visceral, one might even say pathological hatred of "intelligent design" and would sell their own parents and children into sexual slavery in order to keep the Truth © from being presented.

quote:
I might get rhrain or (whatever he posts as)

Um, are you in second grade? Is your argument so pathetic that the only way you can continue is to play stupid games with my name?

(*le sigh*)

quote:
If I saw him in person I would put my hand up to interrupt him and say, "All you have to do is show me or direct me to a model of how one of them evolved with a step by step Darwinian fashion."

Already done. You have read the relevant journal articles, haven't you?

-----

The evolution of adaptive immunity.

Pancer Z, Cooper MD.

Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA. pancer@comb.umbi.umd.edu

Approximately 500 mya two types of recombinatorial adaptive immune systems appeared in vertebrates. Jawed vertebrates generate a diverse repertoire of B and T cell antigen receptors through the rearrangement of immunoglobulin V, D, and J gene fragments, whereas jawless fish assemble their variable lymphocyte receptors through recombinatorial usage of leucine-rich repeat (LRR) modular units. Invariant germ line-encoded, LRR-containing proteins are pivotal mediators of microbial recognition throughout the plant and animal kingdoms. Whereas the genomes of plants and deuterostome and chordate invertebrates harbor large arsenals of recognition receptors primarily encoding LRR-containing proteins, relatively few innate pattern recognition receptors suffice for survival of pathogen-infected nematodes, insects, and vertebrates. The appearance of a lymphocyte-based recombinatorial system of anticipatory immunity in the vertebrates may have been driven by a need to facilitate developmental and morphological plasticity in addition to the advantage conferred by the ability to recognize a larger portion of the antigenic world.

PMID: 16551257 [PubMed - indexed for MEDLINE]

-----

The evolution of adaptive immune systems.

Cooper MD, Alder MN.

Division of Developmental and Clinical Immunology, Departments of Medicine, Microbiology, Pediatrics, and Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA. max.cooper@ccc.uab.edu

A clonally diverse anticipatory repertoire in which each lymphocyte bears a unique antigen receptor is the central feature of the adaptive immune system that evolved in our vertebrate ancestors. The survival advantage gained through adding this type of adaptive immune system to a pre-existing innate immune system led to the evolution of alternative ways for lymphocytes to generate diverse antigen receptors for use in recognizing and repelling pathogen invaders. All jawed vertebrates assemble their antigen-receptor genes through recombinatorial rearrangement of different immunoglobulin or T cell receptor gene segments. The surviving jawless vertebrates, lampreys and hagfish, instead solved the receptor diversification problem by the recombinatorial assembly of leucine-rich-repeat genetic modules to encode variable lymphocyte receptors. The convergent evolution of these remarkably different adaptive immune systems involved innovative genetic modification of innate-immune-system components.

PMID: 16497590 [PubMed - indexed for MEDLINE]

-----

Reconstructing immune phylogeny: new perspectives.

Litman GW, Cannon JP, Dishaw LJ.

Department of Pediatrics, University of South Florida College of Medicine, All Children's Hospital Children's Research Institute, 830 First Street South, Saint Petersburg, Florida 33701, USA. litmang@allkids.org

Numerous studies of the mammalian immune system have begun to uncover profound interrelationships, as well as fundamental differences, between the adaptive and innate systems of immune recognition. Coincident with these investigations, the increasing experimental accessibility of non-mammalian jawed vertebrates, jawless vertebrates, protochordates and invertebrates has provided intriguing new information regarding the likely patterns of emergence of immune-related molecules during metazoan phylogeny, as well as the evolution of alternative mechanisms for receptor diversification. Such findings blur traditional distinctions between adaptive and innate immunity and emphasize that, throughout evolution, the immune system has used a remarkably extensive variety of solutions to meet fundamentally similar requirements for host protection.

PMID: 16261174 [PubMed - indexed for MEDLINE]

-----

On the origins of the adaptive immune system: novel insights from invertebrates and cold-blooded vertebrates.

Kasahara M, Suzuki T, Pasquier LD.

Department of Biosystems Science, School of Advanced Sciences, The Graduate University for Advanced Studies (Sokendai), Shonan Village, Hayama 240-0193, Japan. kasahara@soken.ac.jp

When and how adaptive immunity emerged is one of the fundamental questions in immunology. Accumulated evidence suggests that the key components of adaptive immunity, rearranging receptor genes and the MHC, are unique to jawed vertebrates. Recent studies in protochordates, in particular, the draft genome sequence of the ascidian Ciona intestinalis, are providing important clues for understanding the origin of antigen receptors and the MHC. We discuss a group of newly identified protochordate genes along with some cold-blooded vertebrate genes, the ancestors of which might have provided key elements of antigen receptors. The organization of the proto-MHCs in protochordates provides convincing evidence that the MHC regions of jawed vertebrates emerged as a result of two rounds of chromosomal duplication.

PMID: 15102370 [PubMed - indexed for MEDLINE]

-----

New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system.

Kasahara M.

Department of Biochemistry, Hokkaido University School of Medicine, Sapporo, Japan. kasahara@hucc.hokudai.ac.jp

Recently, it became clear that the human and mouse genomes contain at least three regions paralogous to the major histocompatibility complex (MHC) region. This observation led us to the proposal that the MHC region emerged as a result of chromosomal duplication that took place at an early stage of vertebrate evolution. Here I briefly review this proposal. Accumulating evidence indicates that (a) genome-wide duplication(s) took place close to the origins of vertebrates. Taking this and others into account, I suggest that the duplication(s) involving the MHC region probably took place as a part of the genome-wide duplication(s). The human T cell receptor (TCR) and immunoglobulin (Ig) genes also appear to be located on paralogous chromosomal segments. These findings raise the possibility that the genome-wide duplication provided a major impetus not only to the emergence of the full-fledged MHC system, but also to the appearance of other key molecules of the adaptive immune system such as TCR and Ig.

PMID: 9420471 [PubMed - indexed for MEDLINE]

-----

Mechanisms of antigen receptor evolution.

Eason DD, Cannon JP, Haire RN, Rast JP, Ostrov DA, Litman GW.

Department of Pediatrics, Children's Research Institute, University of South Florida College of Medicine, 830 First Street South, St. Petersburg, FL 33701, USA.

The adaptive immune system, which utilizes RAG-mediated recombination to diversify immune receptors, arose in ancestors of the jawed vertebrates approximately 500 million years ago. Homologs of immunoglobulins (Igs), T cell antigen receptors (TCRs), major histocompatibility complex (MHC) I and II, and the recombination activating genes (RAGs) have been identified in all extant classes of jawed vertebrates; however, no definitive ortholog of any of these genes has been identified in jawless vertebrates or invertebrates. Although the identity of the "primoridal" receptor that likely was interrupted by the recombination mechanism in the common ancestor of jawed vertebrates may never be established, many different families of genes that exhibit predicted characteristics of such a receptor have been described both within and outside the jawed vertebrates. Various model systems point toward a range of immune receptor diversity, encompassing many different families of recognition molecules, including non-diversified and diversified Ig-type variable (V) regions, as well as diversified VJ domains, whose functions are integrated in an organism's response to pathogenic invasion. The transition from the primordial antigen receptor to the monomeric Ig-/TCR-like domain and subsequent antigen-specific heterodimer likely involved progressive refinement of unique intermolecular associations in parallel with the acquisition of combinatorial diversity and antigen-specific recognition through somatic modification of the V region. RAG-mediated recombination and associated junctional diversification of both Ig and TCR genes occurs in all jawed vertebrates. In the case of Igs, somatic variation is expanded further through class switching, gene conversion, and somatic hypermutation. Various approaches, including both genomic and protein functional analyses, currently are being applied in jawless vertebrates, protochordates and other invertebrate deuterostome model systems in order to examine both RAG-mediated and alternative forms of antigen receptor diversification. Such studies have uncovered previously unknown mechanisms of generating receptor diversity.

PMID: 15522620 [PubMed - indexed for MEDLINE]

----

And that was without even trying. When are you going to start doing your homework?

Basically, your argument comes down to: "Because we don't know everything, that means we know nothing."


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 253 by traderdrew, posted 08-30-2009 1:00 PM traderdrew has responded

Replies to this message:
 Message 260 by traderdrew, posted 08-31-2009 11:11 AM Rrhain has responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 270 of 458 (522231)
09-01-2009 11:09 PM
Reply to: Message 258 by traderdrew
08-31-2009 10:49 AM


traderdrew writes:

quote:
I wonder what are the chances of a series of random mutations hitting only the third position in a chain of amino acids.

Actually, it's quite high. The mechanisms the cell has for mutation detection and repair tend to be not nearly as picky about the third codon.

Now, before you go on a "See! Design!" hyperventilation, ask yourself: Why does the cell need mechanisms for detecting and repairing mutation?

Now, please note that Signature in the Cell is a popular press book, not an actual journal article. Take its protestations with massive amounts of salt.

quote:
The article Meyer wrote that was published in Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). I believe the man who had PhDs who authorized it had his keys taken away and was transferred to a hostile supervisor.

Incorrect. First, you're thinking of Richard Sternberg, the managing editor of the journal that published the Meyer article.

Second, there was no persecution of Sternberg. He put an article in the journal that not only hadn't been peer reviewed, it was completely outside the scope of the journal:

The paper by Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," in vol. 117, no. 2, pp. 213-239 of the Proceedings of the Biological Society of Washington, was published at the discretion of the former editor, Richard v. Sternberg. Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The Council, which includes officers, elected councilors, and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history.

The journal is about taxonomy but the paper is about the Cambrian explosion. This is not the journal to publish it in.

Sternberg then claims discrimination from the Smithsonian, but all of his claims are false. First, he held an unpaid position as a research associate. He wasn't fired as he wasn't an employee, but beyond that he certainly wasn't dismissed, either. In fact, he had resigned from the position of editor six months before the edition was published (lead time). But not only did he remain in his position as research associate, the Smithsonian actually extended it to the end of 2006. However, he never showed up.

His actual job at the NIH was never in jeopardy, his pay did not change, and he wasn't fired over it.

Regarding the claim that he "had his keys taken away," that simply isn't true. Instead, there was a reorganization of the entire office space: 17 people and 20 offices were adjusted. He knew about the reorg long before the article was published:

“As you know, as part of an effort to enhance security at the Museum, all researchers were asked to return their keys in 2004, and were issued coded identification badges to provide access to non-public areas. The badge you were issued, which provides general access to doors and elevators, is still operative. If you have any problems gaining access to conduct your research, however please contact the Security office at NMNH. In accordance with NMNH policy, please return your old keys as soon as possible to your sponsor, Dr. Vari.”

-- Smithsonian Deputy Secretary & Chief Operating Officer Sheila Burke

He has lied about the report from the Office of Special Council.

quote:
Most everyone would fear negative reprocussions for publishing an ID article in a journal like that one.

You mean somebody said something not so nice but he wasn't affected in his life in any way? That's sufficient to cause IDers to run screaming into the hills?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 258 by traderdrew, posted 08-31-2009 10:49 AM traderdrew has responded

Replies to this message:
 Message 284 by traderdrew, posted 09-04-2009 11:13 AM Rrhain has responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 271 of 458 (522233)
09-01-2009 11:36 PM
Reply to: Message 260 by traderdrew
08-31-2009 11:11 AM


traderdrew responds to me:

quote:
Here is information leading to a famous one.

(*chuckle*)

You do realize that the paper was retracted, yes?

Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The Council, which includes officers, elected councilors, and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history.

-- Council of the Biological Society of Washington

Not only was the paper simply bad, it was inappropriate for the PBSW:

Systematics (the study of taxonomy) is the subject of the PBSW and it is the subject of Sternberg’s expertise, but it is not the subject of Meyer’s paper. The primary subject of the paper is the Cambrian explosion and, ostensibly, bioinformatics as it pertains to the origin of the higher phyla. This is not the focus of Sternberg’s research, nor does it have much of anything to do with systematics other than an obligatory discussion of how many phyla and sub-phyla originated during the Cambrian. The most appropriate reviewers, then, would be paleontologists. Among the associate editors at the time (and still today) was Gale Bishop, an expert in invertebrate paleontology. There were three other specialists on invertebrates among the associate editors as well, including current PBSW editor Stephen Gardiner, Christopher Boyko and Janet Reid, all specialists in invertebrate zoology (the Cambrian fauna was almost entirely made up of invertebrates). Yet Sternberg felt no need to let any of those people, all more qualified than him on the subject, even look at the paper, or even make them aware of its existence. He may not have been under any formal obligation to send the article to someone with a specialty in Cambrian paleontology, but that is both the professional and the ethical thing to do.

-- Ed Brayton

quote:
It is about time you posted some meaty information.

I am not here to do your homework for you. You're the one saying that there is actual science behind ID. It is your responsibility to justify that claim.

quote:
I see it is about the immune system. I don't have a dog in that complex fight although I know Behe wrote about it. This thread is about information anyway.

Ah, changing the goalposts, are we? You wrote, and I quote Message 253:

If I saw him in person I would put my hand up to interrupt him and say, "All you have to do is show me or direct me to a model of how one of them evolved with a step by step Darwinian fashion."

Well, there you go. The very thing you demanded to see and now you're hoping that you can whine about how it isn't about this other subject and we'll all forget that you didn't ask for that in the first place.

The very thing you claim hasn't been shown has been shown.

So what does that do to your argument?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 260 by traderdrew, posted 08-31-2009 11:11 AM traderdrew has responded

Replies to this message:
 Message 285 by traderdrew, posted 09-04-2009 11:19 AM Rrhain has responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 295 of 458 (522784)
09-04-2009 9:16 PM
Reply to: Message 293 by LucyTheApe
09-04-2009 6:57 PM


LucyTheApe responds to Coyote:

quote:
quote:
But information can be created by random change and by eliminating everything that is not information.

When you say, "random chance"


No, not "random chance," random CHANGE.

quote:
I take it you're referring to probability.

No, not probability. Chemistry. No chemical reaction is ever perfect every single time. When I take two moles of hydrogen gas and a mole of oxygen gas, mix them at STP, and spark the mixture, the heavily favored reaction is water, but you will find some hydrogen peroxide in there as well as some hydronium. Which molecules will be the ones that don't go in the most favored reaction cannot be predicted. They are random.

The reproduction of the cell is a chemical reaction. Thus, it will never happen perfectly every single time. Thus, there will be changes between the parent cell and the daughter cells.

Or are you saying that there is something happening in cell reproduction other than chemistry?

quote:
Do the dice create the information or do you?

Does it matter? You're still ignoring the fact that we're talking about chemistry. The molecules are interacting with themselves. The products of one set of reactions become the reagents for another set of reactions. Some chemical reactions are self-replicating and autocatalyzing.

The "information" comes from the chemicals reacting with themselves. There is no outside consciousness involved.

Or are you saying that there is something going on inside the cell other than chemistry?

quote:
Coyote, it's a scientific endevour.

So where's your science? Why is it that nowhere in any of the biological treatises on the subject can we find anything like what you are proposing?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 293 by LucyTheApe, posted 09-04-2009 6:57 PM LucyTheApe has responded

Replies to this message:
 Message 302 by LucyTheApe, posted 09-05-2009 11:45 AM Rrhain has responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 296 of 458 (522786)
09-04-2009 9:51 PM
Reply to: Message 284 by traderdrew
09-04-2009 11:13 AM


traderdrew responds to me:

quote:
It could me another example of something that lends a bit of support to ID.

Now, I asked you nicely to stop before going on a "See! Design!" hyperventilation.

Why would the cell need a correction mechanism if there weren't mistakes being made in the replication of the cell?

quote:
The error correction mechanisms could be designed for emphasization toward the first or second positions in the codons.

But why? Why would the cell need this sort of thing in the first place?

You need to deal with that first. Then, you'll understand why a correction mechanism exists that allows slop in the third position where it doesn't matter nearly as much as the first or second position.

quote:
As for your comments on Richard Sternberg, I just did a little more investigating myself.

And thus, you found out that he lied about his experience, right? That there was no plot against him, he was not fired, he was not asked to leave his office for any reason other than the entire office was being reorganised, his keys were being taken because he was being given a new card swipe, etc.

Right?

Do you have any evidence to contradict the report from the Smithsonian? The statement from the NIH? From the PBSW? Yeah, you may have read the Washington Post story, but did you actually read the OSC report and see how Sternberg lied about what it said?

So far, all you've done is use Sternberg's secondary statements to back up his primary ones. You do realize that this is circular reasoning, yes? You are claiming that Sternberg's account is accurate because Sternberg says he's not lying.

On the other side, we have independent statements from multiple sources, none of which have anything to do with the other, all of which contradict Sternberg's claims.

It's time for you to explain why you accept Sternberg's claims when it is very clear he has an agenda to push as composed to multiple independent sources, none of whom have any agenda to push.

Of course, it doesn't help that the very director of the OSC was under investigation for the very types of political bias that Sternberg is trying to claim was being inflicted upon him. You say you'll accept NPR...did you find the story from "All Things Considered" about the suit filed against Bloch from his own staff to have him removed?

So the questions are very simple:

Was Sternberg fired from his position as editor or did he resign on his own?
When did his departure as editor happen?
Why was his office changed?
Why was he asked to turn in keys?
Was Sternberg ever denied access to Smithsonian research materials?
Was Sternberg's contract as a research associate at the Smithsonian revoked or extended?

These were the things that the OSC wanted investigated. Do you claim that the results of that investigation showed Sternberg experienced retaliation? If so, upon what basis do you make this claim?

I am not here to do your homework. You need to get past reading what other people tell you what happened and take a look at the first-hand evidence.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 284 by traderdrew, posted 09-04-2009 11:13 AM traderdrew has responded

Replies to this message:
 Message 309 by traderdrew, posted 09-07-2009 11:21 AM Rrhain has responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 297 of 458 (522787)
09-04-2009 10:07 PM
Reply to: Message 285 by traderdrew
09-04-2009 11:19 AM


traderdrew responds to me:

quote:
This thread is about information anyway.

Then why did you bring it up? You thought you could catch us in some sort of bind and now that you have seen that your argument is falling apart, you're backpedaling like hell, hoping that nobody will notice.

quote:
Can you discern the difference between rhetorical arguments and substance?

(*chuckle*)

Nice try, but that's our argument to you. You haven't presented anything of substance. It's been nothing but flourish and hand-waving. You're doing it right now. You painted yourself into a corner and rather than simply admit you made a mistake, that the Meyer article was published under false pretenses and yet despite that, nobody suffered any consequences because of it, you're trying to whine and complain that we're "off topic" when you were the one who brought it up in the first place.

quote:
Can we stop with equivocation

And thus, you prove my point. Do you even know what that word means? Where is the word with a double meaning that you are concerned about?

No, you threw that word in to try and show that you had some "substance" to your post when it was nothing more than the "rhetoric" that you are complaining about.

That said, how sad that you find rhetoric to be somthing to avoided. The reason that we can have any sort of actual discussion of anything is because of rhetoric. "Rhetoric" is not a synonym for "worthless argument." The fact that somebody can dazzle you with fancy bullshit isn't the fault of rhetoric. It's simply that you can be dazzled. No rhetorical framework can prop up a faulty argument:

Was there any retaliation against Sternberg? If so, what was it? Was he fired from his editing position or did he resign? When did he leave his position as editor? Why was he asked to turn in his keys? Why was his office reassigned? Was he fired as an associate researcher from the Smithsonian? Was he ever denied access to the research materials there? Was his job at the NIH ever in any jeopardy? Was he demoted? Did his pay change?

If not, under what justification do we claim that he sufference any negative effects for his publication of a non-peer reviewed article in an inappropriate journal?

quote:
and get back to the subject matter?

If you didn't mean to talk about this, why did you bring it up?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 285 by traderdrew, posted 09-04-2009 11:19 AM traderdrew has not yet responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 305 of 458 (522861)
09-05-2009 6:51 PM
Reply to: Message 302 by LucyTheApe
09-05-2009 11:45 AM


LucyTheApe responds to me:

quote:
They are not random they are probabilistic.

Do you even know what the term "probabilistic" means? Or are you just throwing it out in hopes of dazzling me with bullshit? I am a mathematician. My specialty was numerical modeling. I know a fair about about probability and statistics.

They are random. There isn't a "probability" regarding the products of the reaction. That's because the chemistry is a forcing process. You don't get hydrogen peroxide out of the reaction unless the conditions allow it. That is a factor of local conditions combined with the reactivity traits of oxygen and hydrogen. The reason why water is the favored product is because the local conditions are overwhelmingly such that the reactive traits of oxygen and hydrogen force a result of the oxygen and hydrogen molecules splitting and then recombining to form water:

2H2 + O2 -> 2H2O

But because the mixture is not uniform, because there are variations, because the energy distribution is not perfectly even as the reaction travels across the gas mixture, sometimes we get another reaction:

H2 + O2 -> H2O2

This isn't a question of "probability." It is forced due to the nature of chemistry. We cannot assign any probability to any given atom about what will happen to it because it is so dependent upon local conditions. Once those local conditions resolve, the reaction is forced.

quote:
Chemical reactions are also entropic whereas the cell is antientropic.

OK...it is clear you don't know what those terms mean.

Very simple: What is "entropy"? Hint: If your answer includes any of the words "order," "disorder," or "information," then your answer is incorrect. No, don't look it up. I am not interested in what you can quote from someone else. I want to hear it in your own words:

Starting from first principles of thermodynamics, what is the definition of entropy? Along those lines, what is the opposite of entropy?

Have you ever heard of "Gibbs Free Energy"? What does it have to do with chemical reactions? How exactly does the cell find the energy it needs to function? You have heard of the citric acid cycle, yes? Cellular respiration? Photosynthesis? Fermentation? Glycolysis? ATP? NAD? Pyruvate?

Can you draw out the free energy levels for each of the steps in glycolysis and respiration?

Do you have any idea what "entropic" means?

quote:
To create new information is counter entropic.

So since "new information" is a forced result of chemical reactions, what is the problem?

Which has more "information": A or AA?
Which has more "information": A or B?
Which has more "information": A or AB?

Or are you saying that something is going on inside the cell other than chemistry?

quote:
Chemicals contain no information, they're just chemicals subject to the natural laws.

So are you saying that there is something going on inside the cell other than chemistry?

quote:
Why do you make such a silly statement when you don't even believe it yourself.

You're the one that's talking about "information," not me. I'm the one saying that the cell is simply a place where some interesting chemistry takes place.

Are you saying that there is something going on inside the cell other than chemistry?

quote:
Information requires an encoder a decoder and a language, none of these are present in matter but are all present in the cell.

I'm going to keep on asking until you answer:

Is there something going on inside the cell other than chemistry? There is something other than matter in a cell?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 302 by LucyTheApe, posted 09-05-2009 11:45 AM LucyTheApe has not yet responded

Replies to this message:
 Message 306 by greyseal, posted 09-06-2009 11:40 AM Rrhain has not yet responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 311 of 458 (523102)
09-08-2009 1:12 PM
Reply to: Message 309 by traderdrew
09-07-2009 11:21 AM


traderdrew responds to me:

quote:
A designer would have designed a perfect one right?

Well, a designer can do anything in any way, which is why it isn't really an answer. No matter what results we get, no matter what observations we actually see, a designer that can do anything doesn't really explain anything.

An answer that explains everything actually explains nothing.

Before we even get to the question of why the mechanism isn't perfect, the question for you is why would the cell need a correction mechanism for chromosomal replication in the first place?

quote:
In other words, "How perfect does perfect have to be?"

You do realize that "perfect" is like "unique," yes? One cannot be "more" perfect. You either are perfect or you are not.

Why would the cell need a correction mechanism in the first place?

quote:
Error correction mechanisms should help correct the damage.

Yes, but why? Why would these things have any effect in the first place? Why is there any possibility for the chemical reaction to take place in any other way?

quote:
Why does lying about the events disprove design?????

In and of itself, it doesn't. But it does call his ability to be honest about what he is talking about into question. If he is going to lie about what happened to him when he published the paper, exactly how honest can we expect him to be about why he published it? Since the review process for the paper was not followed, exactly how trustworthy can we expect to find the paper?

It might have a point, but we have no way of knowing it because everything about how this paper came to be has been tainted. We'll have to start over from the very beginning. There's a reason we subject papers to peer review and don't just publish anything.

quote:
What matters is the information in that article and you people need to refute that content. Where is your common sense?

Nice try, but that's our argument to you. Common sense indicates that a paper that was specifically and deliberately taken outside of the normal processes of review, inserted into a journal that it has no business being in, and to have the person who did it go off on a screaming tirade about how oppressed he is when absolutely nothing happened to him is indicative that there is something very suspect about this paper, especially since it runs counter to every other result we have ever found.

Common sense would indicate that Meyer needs to go back to the drawing board, resubmit his paper to an appropriate journal, have it go under proper review, and then see where we are. Those who propose "ID" are the ones who need to come up with the proof. This paper might be it but it hasn't been properly examined.

Nobody gets the benefit of the doubt in science. All claims are met with skepticism since justification is always required. So far, "ID" has yet to provide one single piece of evidence to justify itself.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 309 by traderdrew, posted 09-07-2009 11:21 AM traderdrew has not yet responded

Replies to this message:
 Message 323 by Wounded King, posted 09-09-2009 4:32 AM Rrhain has not yet responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 338 of 458 (523406)
09-10-2009 2:58 AM
Reply to: Message 333 by traderdrew
09-09-2009 12:10 PM


traderdrew writes:

quote:
"dials for adjusting laws of physics"

Do you have any evidence of any other universe? The very second sentence of your own source is:

There is no firm scientific consensus that the fine-tuning hypothesis is correct.

So unless you can show that there is a second universe out there, then we are left with only the universe we have.

And thus, the probability of a universe existing with precisely the characteristics of our current universe is exactly 1.

quote:
The anthropic principles are the best arguments against it that I can think of.

The anthropic principle is nothing more than a tautology: Of course we exist in a universe that is capable of supporting our existence. Where else could we possibly exist?

A parent and child are walking along when the child asks, "Why is the sky blue?"

The parent responds, "Because if it were green, we would ask, 'Why is the sky green?'"

That is what you are arguing: That the reason the sky is blue is specifically and solely so that one carbon-based organism upon its surface can make an acoustic waveform of "hwai Iz thuh skai blu."

If it seems ridiculous to claim that the entire universe was created so that one person could ask, in English, "Why is the sky blue?" then it is equally ridiculous to claim that it was all created so that the persons could exist within it.

But just in case you've forgotten, you need to show that there is a second universe out there.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 333 by traderdrew, posted 09-09-2009 12:10 PM traderdrew has responded

Replies to this message:
 Message 346 by traderdrew, posted 09-11-2009 11:57 AM Rrhain has responded

  
Rrhain
Member (Idle past 185 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 350 of 458 (523691)
09-11-2009 11:09 PM
Reply to: Message 346 by traderdrew
09-11-2009 11:57 AM


traderdrew responds to me:

quote:
quote:
So unless you can show that there is a second universe out there, then we are left with only the universe we have. And thus, the probability of a universe existing with precisely the characteristics of our current universe is exactly 1.

Fine... I have no problem dealing with a single three dimensional universe or a multiuniverse around here.


Huh? What on earth does that have to do with what I said?

The question to you is whether or not there is another universe out there. Certain aspects of quantum theory and cosmology seem to point to the possibility of other universes out there, but we don't have any evidence of them so far.

I wouldn't be so quick to applaud the idea of multiple universes, though, since such theories tend to indicate that there can be as many universes as you like. Which means that a universe exactly like the one we are currently living in are inevitable.

But no matter what, you run into the problem of the anthropic principle: Of course we exist in a universe that allows for our existence. Where else could we possibly be?

quote:
Need I say more? Now, how can we argue with these two scientists???

Because I'm a scientist, too. And surely you're not about to try and pull the argument from authority on me, are you?

After all, Hoyle rejected the Big Bang which has been so soundly shown that it would be perverse to deny it.

Too, Hoyle thinks life originated in space, advocating panspermia, with evolution on earth driven by viruses arriving from comets.

Are you sure you want to hitch your wagon to that fallen star?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 346 by traderdrew, posted 09-11-2009 11:57 AM traderdrew has not yet responded

  
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