Shapiro has published scientific articles with Richard Sternberg who advocates a similar position but who has become one of the poster boys of the Discovery Institute and one of the stars of the movie Expelled: No Intelligence Allowed. Like Sternberg, Shapiro is admired by IDiots [Non-supernatural ID?: University of Chicago microbiologist James Shapiro works with ID guys, dismisses Darwinism, offers third way].
One of the characteristics Shapiro shares with the IDiots is attacking evolution. In this post I want to review a paper he published in 2009 on "Revisiting the Central Dogma in the 21st Century" (Shapiro, 2009).
The correct version of the Central Dogma of Molecular Biology is:
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)In other words, the flow of information is from nucleic acid to protein and never from protein to nucleic acid.
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
The incorrect version of the Central Dogma of Molecular Biology is what Crick referred to as the "Sequence Hypothesis" and what we now know as a simplified version of the standard pathway for information flow from genes that specify a protein product. The incorrect version is often presented in textbooks as the real Central Dogma although that's slowly changing [The Central Dogma Strawman].None of this should be a problem for someone who is writing a scholarly article for the scientific literature since we expect such a person to have read the relevant references (Crick, 1958; Crick, 1970). They should get it right. Let's see how Shapiro does when he says ...
The concept was that information basically flows from DNA to RNA to protein, which determines the cellular and organismal phenotype. While it was considered a theoretical possibility that RNA could transfer information to DNA, information transfer from proteins to DNA, RNA, of other proteins was considered outside the dogma and "would shake the whole intellectual basis of molecular biology [Crick, 1970].That sounds pretty good but the first part is a little troubling. Which version does Shapiro actually believe he's "revisiting"?
For that we have to look to a paper he published last year (Shapiro, 2010) where he says ...
Crick's central dogma of molecular biology:Oh dear, he's got the wrong version. This doesn't look good.
1. DNA --> 2x DNA
2. DNA --> RNA --> protein --> phenotype
The 2009 paper lists a whole bunch of things wrong with the central dogma but I'll just mention the ones under "Basic Molecular Functions."
The molecular analysis of fundamental biochemical processes in living cells has repeatedly produced surprises about unexpected (or even "forbidden") activities. A short (and partial) list of these activities provides may illustrative complications or contradictions of the central dogma.None of these things complicate or contradict the correct version of the Central Dogma of Molecular Biology. They don't even conflict with the general flow of information diagram that we see in the textbooks since that diagram is meant to represent a simple version of information flow from DNA to protein. The fact that some species might have a few extra adornments isn't really a problem. Biology is full of exceptions to general rules.
- Reverse transcription ....
- Posttranscriptional RNA processing ....
- Catalytic RNA ....
- Genome-wide (pervasive) transcription ....
- Posttranslational protein modification ....
- DNA proofreading and repair ....
The fact that he mentions reverse transcription is especially revealing since the reason why Francis Crick wrote his 1970 Nature paper was to dispel the notion that reverse transcription had anything to do with the Central Dogma of Molecular Biology. You only need to read the opening paragraph of that 41-year old paper to see how little things have changed.
Plus ça change (plus c'est la même chose)."The central dogma, enunciated by Crick in 1958 and the keystone of molecular biology ever since, is likely to prove a considerable over-simplification".This quotation is taken from the beginning of an unsigned article [1] headed "Central dogma reversed", recounting the very important work of Dr. Howard Temin [2] and others [3] showing that an RNA tumour virus can use viral RNA as a template for DNA synthesis. This is not the first time that the idea of the central dogma has been misunderstood, in one way or another. In this article I explain why the term was originally introduced, its true meaning, and state why I think that, properly understood, it is still an idea of fundamental importance.
So, why do people like Shapiro makes such a big deal of this? It's because claims that the Central Dogma of Molecular Biology have been overthrown1 attract attention and fit into a larger agenda. If your goal is to start a revolution in biology then the first thing you have to do is knock down the existing "dogma." It doesn't seem to matter that you are attacking a strawman. But it's a sign that the rest of your agenda isn't very sound.
1. Such claims are occurring with increasing frequency in the past ten years. It now seems that the central dogma is being falsified about three or four times a year.
Crick, F.H.C. (1958) On protein synthesis. Symp
Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227:561-563. [PDF file]
Shapiro, James A. (2009) Revisiting the Central Dogma in the 21st Century. Ann. N.y. Acd. Sci. 1178:6-28. [doi: 10.1111/j.1749-6632.2009.04990.x]
Shapiro, J.A. (2010) Mobile DNA and evolution in the 21st century. Mob DNA. 1:1-14. [doi: 10.1186/1759-8753-1-4]
544 comments :
«Oldest ‹Older 201 – 400 of 544 Newer› Newest»Lou Jost posted:
"so yes, given enough time, that common ancestor could evolve into things as different as goats and horses on different isolated mountaintops.
That takes more faith than I can muster. And I have studied these ideas for many years so I know all the arguments.
If you were to talk about major genetic re-engineering saltations leading to a new type of creature, then I am with you. But if you think that simply being on separate mountaintops etc will bring about horses, llamas etc from some other different type of creature then I am not with you.
But I know that you are stuck in the box that things MUST have happened a certain way. Not because it is plausible that they happened that way but because your theory dictates it.
Whatever aspect of this we discuss you will use your intelligence (which is formidable) to make up some sort of explanation (some story) to shoehorn it into your pre-existing theory. Even if that shoehorning is not plausible.
And at the end of it you will still not have an explanation as to why things happened as they did. Just a description of how you think the mechanics worked.
There is another way of looking at all of this which does justice to all the evidence and is consistent with, for example what Pagel and Shapiro have found.
No, Anon, when I say that I common descent is a fact, I am basing that on evidence, from the genome to the fossil record. The question of HOW evolution happens is a separate one.
I gladly welcome new ideas on how variation might arise in the genome. That only makes my goats turn into bears faster on those mountain tops.
Lou Jost writes:
If you don't believe the evidence for common ancestry of mammals, then indeed you are lost and need to do some reading. I hope that is not your position.
Depends which part of which thread Anonymous is in. He's argued strenuously against common ancestry, and also made lengthy arguments that hinge upon it being true.
Allan, thanks for the tip to RDF but I was actually hoping for a more technical forum for people working in population genetics and evolution
's OK, I knew it wasn't quite what you were after - something meatier than recreational disputation! But it would be a good spot for Anonymous to try his hand.
Common ancestry makes perfect sense.
But "common ancestry" can have different meanings. So one has to be careful.
Lou Jost posted:
"I gladly welcome new ideas on how variation might arise in the genome. That only makes my goats turn into bears faster on those mountain tops."
If you work with the idea that the intelligence of Nature can work through saltation-type genetic engineering, then you no longer need all that mountain-top type "explanation" falderal
@Anonymous,
I think you have limited yourself by only considering those isolation mechanisms that require the earth to move under a species. But it is worth remembering that species move about its surface also. Ranges ebb and flow for all manner of reasons. For a sexual population, a requirement for remaining a single species is constant stirring. This and mating are the only things that act to homogenise, and keep a 'consensus' genome. Everything else acts towards fragmentation.
Think of a species as an irregularly-shaped blanket, full of holes and threadbare patches. Competitive species, predators, diseases, climate change etc are constantly pulling at the threads. Even though individuals can move, genes cannot survive long in regions where there are no mates - where the 'blanket' is too thin or non-existent.
By constant movement, mating and recombination, a species retains some degree of uniformity. But it is constantly under threat of fragmentation due to different random (stochastic) mutation/fixation processes ongoing in different parts of the range. All that is needed is a break in the 'fabric' - even simple stochastic fluctuation can do this - and the mixing has been turned off. It may only be temporary, but it is the beginning of a process that may result in speciation - that is, even if the subpopulations subsequently remix, genetic divergence alone has become the sufficient cause for eternal reproductive isolation. A mountain range or a river will do it, but so will many other things.
What people do not acknowledge is that the position I have outlined is logical, parsimonious and consistent with all evidence.
People reject (disdain actually) what I say because they simply do not believe that Nature could be intelligent. And also it is a different idea than the one they were taught. That is a different position than disagreeing on the basis of logic or evidence.
Allan Miller posted:
"All that is needed is a break in the 'fabric' - even simple stochastic fluctuation can do this - and the mixing has been turned off. It may only be temporary, but it is the beginning of a process that may result in speciation - that is, even if the subpopulations subsequently remix, genetic divergence alone has become the sufficient cause for eternal reproductive isolation. A mountain range or a river will do it, but so will many other things."
Sure, subgroups of a larger group can get spread out. At that point you have separated groups of the same type of creature. But you have no greater likelihood that the split-off group will evolve into a different type of creature than you had originally. Perhaps less, because as Moran told us, groups (eg. subgroups) less than 1,000 will likely go extinct.
The original problem is unchanged.
The idea that you and others are expressing is really not a plausible idea.
Anonymous: "What people do not acknowledge is that the position I have outlined is logical, parsimonious and consistent with all evidence."
- We are waiting for you to (a) outline your position beyond stating "saltation" and "intelligence of nature", and (b) explain any of the situations we have highlighted that do not seem even remotely "intelligent".
"People reject (disdain actually) what I say because they simply do not believe that Nature could be intelligent."
- We have neither a need nor a proposed mechanism for such a hypothesis. You might as well say it was "magic" or "fairy dust". We do not disdain what you say, we disdain what you refuse to say and the manner in which you do it, I.e. Ignoring anything you do not like.
"And also it is a different idea than the one they were taught."
- True. I was taught by scientists, using scientific methods and relying on data not fantasy.
"That is a different position than disagreeing on the basis of logic or evidence."
- Not true. Repeating this mantra won't make it any more true!
I posted:
"Sure, subgroups of a larger group can get spread out. At that point you have separated groups of the same type of creature. But you have no greater likelihood that the split-off group will evolve into a different type of creature than you had originally. Perhaps less, because as Moran told us, groups (eg. subgroups) less than 1,000 will likely go extinct.
The original problem is unchanged."
I hope that someone will speak to this because it actually shows how completely superfluous the physical reproductive isolation argument is.
"But you have no greater likelihood that the split-off group will evolve into a different type of creature than you had originally."
Actually, you have approx. double the chance because you now have two populations rather than one. Your speculation about the new population size is purely plucked out of the air. (Plus, small populations are not guaranteed to go extinct and many extant populations appear to have gone through bottlenecks in the past - the most famous example being cheetahs. In fact, through accelerated drift and founder effects, small populations can even evolve faster, potentially increasing the chances further.) What you need, though, is time. A lot of time!
Come on, Anonymous. Get one thing right.
"The idea that you and others are expressing is really not a plausible idea."
Far from being implausible, the idea that Allan Miller summarised so beautifully is well documented and going on even as we type. If it doesn't pass your "smell test", I suggest a reading and comprehension test.
"Actually, you have approx. double the chance because you now have two populations rather than one."
Does anyone see the problem with this logic?
@anon That takes more faith than I can muster.
If it takes faith you're doing it wrong.
Leave that for religion.
"Arguments From Personal Incredulity
Somewhere in his writings Richard Dawkins talks about anti-evolution types who argue from personal incredulity — they say, “I just can’t believe that chance could create something as complex as an eye”, and think that they have scored an important point. All they’ve actually done, of course, is rehash their prejudices. (Simulations show, by the way, that chance plus selection can indeed create an eye, in a relatively short time as evolutionary history goes).
-Paul Krugman"
By the way anonymous if your about to argue that two small independent populations are the same as one large combined population, then your about to look extremely silly.
What people do not acknowledge is that the position I have outlined is logical, parsimonious and consistent with all evidence.
Nope. Cancer as "the equivalent of a criminal intelligence," logical and consistent with the evidence? Yeah, right. The "intelligence of Nature," consistent with Lenski's experimental results, or with principles of fundamental physics? Nope.
And let's talk about "parsimonious." As a wise man once said: You keep using that word. I do not think it means what you think it means.
You keep trying to insert "intelligence," when well-known mathematics, biochemistry and genetics are perfectly adequate. No intelligence needed. Your explanation is therefore not parsimonious, since it adds an unnecessary step.
Anonymous said...
I see that heleen is still being rude and referring to me as "it".
I overlooked that but will stop discussion with him/her.
Anonymous said that before and did not stick to its promise.
Evolutionists argue from personal incredulity in that "they
just can’t believe" that Nature could be intelligent.
"And think that they have scored an important point. All they’ve actually done, of course, is rehash their prejudices."
cabbagesofdoom writes:
Far from being implausible, the idea that Allan Miller summarised so beautifully is well documented and going on even as we type.
Indeed, it's not in the least implausible - something very similar has occurred and continues to occur practically before our eyes in the case of languages under the influences of human migration, geographic isolation, and changes over time (copying errors - "mutations," as it were).
Anonymous said...
What people do not acknowledge is that the position I have outlined is logical, parsimonious and consistent with all evidence.
People reject (disdain actually) what I say because they simply do not believe that Nature could be intelligent.
Actually, Anonymous has not outlined a position, nor has he/she/it made clear anything he/she/it might call his/her/its position logical, or parsimonious or consistent with any evidence.
Logical? How?
Parsimonious? How?
Evidence? Anonymous does not have a clue evidence is, he/she/it only deals in assertions.
Well Anonymous, who is Nature?
What do you call the 'intelligence of Nature'?
How do you propose to find evidence for the 'intelligence of Nature'?
How does 'the intelligence of Nature' work, what is its mechanism/
It is the task of Anonymous to explain in detail. Anonymous has not explained anything of its ideas whatsoever.
Anonymous does not appreciate the difference between evidence and assertion; therefore, Anonymous is not able to explain his/her/its position.
@Anon
I believe actually what we've been saying is that you have no plausible mechanism, no explanation for the origin of this 'intelligence', no compelling evidence that isn't better explained by other means, no detail of any kind and that there exists substantial counter evidence. You on the other hand reject alternatives because of a 'smell test'? Bullshit methinks.
@anus If you work with the idea that the intelligence of Nature can work through saltation-type genetic engineering, then you no longer need all that mountain-top type "explanation" falderal
As long as you're willing to pull "Nature" out of your backside.
"Actually, you have approx. double the chance because you now have two populations rather than one."
Does anyone see the problem with this logic?
The answer is that there are half the number of individuals in each group.
But go on and post your "yes but" responses. I have heard them all before.
I posted:
"Sure, subgroups of a larger group can get spread out. At that point you have separated groups of the same type of creature. But you have no greater likelihood that the split-off group will evolve into a different type of creature than you had originally. Perhaps less, because as Moran told us, groups (eg. subgroups) less than 1,000 will likely go extinct.
The original problem is unchanged."
I hope that someone will speak to this seriously because it actually shows how completely superfluous the physical reproductive isolation argument is.
I said:
"Now we know that proteins (e.g. methyl transferase) are capable of changing sequence information of DNA (e.g. the retrieval of DNA sequence information due to methylation)."
Reply missing the point was:
Methylation of DNA bases does not change the sequence of DNA bases. Crick said that the central dogma (poor word choice on his part) forbade transfer of sequential information (i.e. residue to residue, in some ratio, not necessarily 1:1). Methylation doesn't do that.
Clarification:
Methylation does not change the formation of base sequence, but by rendering bases undreadable does change the "sequence information". As a simplistic metaphor consider using English, if TAGGAGCAT, say, would be rendered unreadable at two G letters, the meaningful information TAG A CAT would emerge.
Science:
Crick was mistaken by using the word Dogma, as he failed school in Latin. He certainly could not have just imported "information" as defined by Shannon - or if he did was plainly mistaken, disregarded Schrodinger's "What is life" in which the aperiodical crystal (DNA) is predicted to contain the code of life by covalent hydrogen bondings, but the encoding of info had not been specified by Schrodinger, and was overlooked by Crick. (One bit is the negative binary logarithm of probability 1/2). Fact is, "genome information" has not been defined, except by FractoGene, see The Principle of Recursive Genome Function popularized in YouTube "Is IT ready for the Dreaded DNA Data Deluge".
Usefulness of New Science:
Cancer is known as the genome disease of uncontrolled growth. The above YouTube shows at min. 30 how aberrant methylation and chromatin modulation, failing to cancel auxiliary info sustaining fractal iterative recursion, results in uncontrolled recursion (cancer).
"If you work with the idea that the intelligence of Nature can work through saltation-type genetic engineering, then you no longer need all that mountain-top type "explanation" falderal"
You have exchanged a perfectly clear and easily verified mechanism for a magic bit of word play that explains nothing.
We showed you how many ways there are to get isolation, and this did not even slow you down. I bet you still think there are not enough isolating mechanisms ("mountains") to account for present diversity, even though we have just proved that there are virtually unlimited opportunities for isolation.
Will you admit that there is no acute shortage of isolating mechanisms? Or will you go on as if nothing happened?
@Anon
There is no need for a "yes but" response because your statements are completely wrong. You seem to be under the misapprehension that individuals evolve instead of population, hence if a population has half as many individuals it has half the chance of generating a new species. This is totally incorrect because the rate of fixation due to either random events or selection is inversely correlated to the population size due to a sampling effect. Perhaps you should consider taking an introduction course in population genetics or statistics, it might do you a world of good.
Anonymous writes:
The original problem is unchanged.
I am amazed that even someone with your nearly complete lack of understanding of genetics can't recognize the very obvious change.
Mutations are always occurring in the members of a population. Due to interbreeding, the population will be genetically interconnected as those changes occur.
Now separate the one population into two. No interbreeding to keep the two populations genetically interconnected as mutations occur and are fixed in the population over generations. The two populations are therefore free to genetically diverge from one another, and inevitably will, perhaps to the point at which they are separate species.
Quite a simple concept. A grade schooler would probably have little trouble with it. So it shouldn't be difficult, unless you happen to be someone who for reasons of his own refuses to understand it.
"Will you admit that there is no acute shortage of isolating mechanisms? Or will you go on as if nothing happened?"
It is not even close. But it is moot. As I have pointed out already:
"Sure, subgroups of a larger group can get spread out. At that point you have separated groups of the same type of creature. But you have no greater likelihood that the split-off group will evolve into a different type of creature than you had originally. Perhaps less, because as Moran told us, groups (eg. subgroups) less than 1,000 will likely go extinct.
The original problem is unchanged."
Anonymous is Doug Dobney aka Socrates aka the Pterosaur to Bird kook
Again with the attempt to disclose personal info.
Moran should really say something about this considering the
Rhett Daniels situation he alerted us to.
I think anus is Pellionisz.
Anon, we just showed you that there are a wide variety of isolation mechanisms, and that they could lead to exponentially increasing numbers of new species over time. And still you cling to your absurdly narrow ideas about isolating mechanisms.
You clearly are not going to think about anything we say, so there is no point in discussing this further with you. Bye.
Dr. Moran I would like to ask you to warn people against trying to disclose personal info. This is getting out of hand.
The Rhett Daniels situation is a really scary reminder of the problem.
Bye Lou Jost.
You are one of the few people here that is able to keep up a decent discussion.
It is still not clear whether people recognize the difference between speciation which is just a new species of the same type of creature on the one hand
and
the speciation of a new type of creature on the other hand.
Evolution theory cannot explain the latter type.
So evolutionists who think there is no need for the intelligence of Nature are fooling themselves. Evolution theory is not capable of explaining the speciation of new types of creatures.
Or perhaps anus is Rhett Daniels.
steve oberski said...
Or perhaps anus is Rhett Daniels.
He is 100% Doug Dobney aka Socrates aka Pterosaur to bird guy
Check out his comments in his blog.
http://pterosaurnet.blogspot.com/
or check out his posting under Socrates at TalkRational.org
There's no doubt who he is.
Here is an interesting article:
http://www.sciencedaily.com/releases/2009/05/090520140408.htm
"The transposons actually perform a central role for the cell," said Laura Landweber, a professor of ecology and evolutionary biology at Princeton and an author of the study. "They stitch together the genes in working form." The work appeared in the May 15 edition of Science."
"Last year, we found the instruction book for how to put this genome back together again -- the instruction set comes in the form of RNA that is passed briefly from parent to offspring and these maternal RNAs provide templates for the rearrangement process," Landweber said. "Now we've been studying the actual machinery involved in the process of cutting and splicing tremendous amounts of DNA. Transposons are very good at that."
The term "junk DNA" was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be."
The cell certainly has tools available for genetic engineering.
For some reason the link did not copy correctly.
Here it is:
http://www.sciencedaily.com/releases/2009/05/090520140408.htm
http://www.sciencedaily.com/releases/2009/05/090520140408.htm
The system changes the link.
See this thread:
http://sandwalk.blogspot.com/2011/08/darwinian-theory-in-nut.html
It might help if the other Anonymous would explain how a major genetic re-engineering saltation could change a pterosaur into a dromaeosaur with no transitional forms whatsoever.
"Evolution theory is not capable of explaining the speciation of new types of creatures."
WRONG! (Old boring wrongness at that.) Go read some Dawkins or Coyne.
"Clarification:
Methylation does not change the formation of base sequence, but by rendering bases undreadable does change the "sequence information". As a simplistic metaphor consider using English, if TAGGAGCAT, say, would be rendered unreadable at two G letters, the meaningful information TAG A CAT would emerge. "
ROFL. The extent of your ignorance of biology really is quite staggering. Go away, read up on methylation, chromatin and gene silencing, and then come back sheepishly and tell us what is SO wrong with your "clarification".
@Anon
If you have one N-member population, you accept it can evolve (within 'type'). But if it splits into two N/2-member populations, evolution stalls because they are half as big ... ???
You don't think there is any scope for new populations to change number, then? Not that it matters; there is no "threshold of evolution".
OK, let's say there is, and that new populations are forever constrained to remain at the size they were when split. Give me a number that you think represents a threshold of evolution vs extinction. Through the power of mathematics, I will tell you how big an ancestral population would need to be to create two 'evolvable' subpopulations by splitting.
Anonymous said...
It is still not clear whether people recognize the difference between speciation which is just a new species of the same type of creature on the one hand
and
the speciation of a new type of creature on the other hand.
Evolution theory cannot explain the latter type.
Of course people (but perhaps not Anonymous) recognize that difference: speciation leads to a new species. That is the definition of speciation. It is what the word means.
'Speciation of a new type of creature' is contrary to everything people (but perhaps not Anonymous) know about speciation.
Evolution theory is not capable of explaining the speciation of new types of creatures.
Evolution does not involve any speciation into 'new types of creatures'.
It is only hindsight and focussing on the present that singles out 'new types of creature'. In its time, Juramaia sinensis was just one of range of animals, and nothing at 160 My ago would have indicated is was a 'new type of creature'.
@Dr. Moran:
The title of this post is:
"Revisting the Central Dogma in the 21st Century"
Revisiting?
Revising?
In between, or both?
Anons posts on talkrational are pretty mind blowing to read. In light of what he has posted here, apparently he's been working on that Mesonychid evolved into canine train of thought for two years!
*Note I didn't use names so no need to whine.
Anonymous said...
Evolution theory is not capable of explaining the speciation of new types of creatures.
Paleontology is capable of tracing the origin of 'new types of creatures', that is, finding the paleontological roots of the present crown groups.
Molecular phylogeny is capable of tracing the origin of 'new types of creatures', that is, finding the molecular roots of the present crown groups.
Together, that gives an understanding of the origin of the present crown groups.
'New types of species' - what is 'new'? A prehensile tail?
Boojum said...
Anons posts on talkrational are pretty mind blowing to read. In light of what he has posted here, apparently he's been working on that Mesonychid evolved into canine train of thought for two years!
*Note I didn't use names so no need to whine.
Some of the stuff on Pagel and that transposon paper from 15 My 2009 are copied and pasted from talkrational.
Actually, people here are quite gently compared to the people on talkrational.
It would appear that the folks here have learned nothing from the Rhett Daniels case.
I wonder if someone here will begin threatening my wife and children as has happened to me and my family elsewhere.
People think this is all a game.
Does it have to happen to you personally before it matters?
I am disappointed that Moran, after alerting us to the Rhett Daniels, situation, does nothing on his own blog.
It is still not clear whether people recognize the difference between speciation which is just a new species of the same type of creature on the one hand
and
the speciation of a new type of creature on the other hand.
Evolution theory cannot explain the latter type.
Natural genetic engineering can handle the first type - as Shapiro has shown. That can be called microevolution.
The genetic engineering of Nature at a higher level is required for the second.
Anus/Socrates, where do you get all that energy ?
10,000 posts !
And you get to cut & paste them pretty much verbatim which saves you a lot of effort.
http://talkrational.org/showthread.php?t=42095
Socrates
Senior Member
Join Date: Oct 2009
Posts: 9,692
Pagel study split from Macroevolution thread
Anonymous said...
It would appear that the folks here have learned nothing from the Rhett Daniels case.
1 I got the impression it is not the 'Rhett Daniels' case, but EpriRen's case. Rhett Daniels was the one to do the threatening.
2 You could have prevented the curiosity by taking any other moniker than Anonymous. Any name would have done. (Snark for instance - we've got a Boojum)
Anonymous said...
It is still not clear whether people recognize the difference between speciation which is just a new species of the same type of creature on the one hand
That is the only meaning of the word speciation.
and
the speciation of a new type of creature on the other hand.
Evolution theory cannot explain the latter type.
Such ‘speciation of a new type of creature’ has never been observed therefore evolution does not need to explain it. ‘A new type of creature’ can only be seen in hindsight (and depends on systematic conventions), and therefore never has to do with speciation.
Natural genetic engineering can handle the first type - as Shapiro has shown. That can be called microevolution.
The genetic engineering of Nature at a higher level is required for the second.
Neither natural genetic engineering exists nor the genetic engineering of Nature at a higher level.
Anonymous has not given any evidence for either. (Shapiro did not show the first).
Dear Anonymous,
Why you think anyone here would care enough to threaten your family, is beyond me. But, as others have pointed out, adopting a pseudonym would deflect most of the curiosity your veil of secrecy invokes.
Perhaps, though, given that you have been thoroughly humoured by many folks here who have taken the time and trouble to give sensible, scientifically sound responses to your questions and comments, perhaps you would have the courtesy to answer a couple of questions of my own. I don't want personal info but I would love to understand you a little better:
1. Why do you post comments here? What do you hope to achieve? It is clear that you are not picking the collective brain of the group for insight or wisdom, for you ignore it all. It is clear that you are not interested in serious scientific discourse for the same reason. It is clear that no one here is going to be magically convinced by your blunt statements of fantasy without any supporting data or theoretical framework. So, why do you do it? It seems to be a colossal waste of time and energy that could be spent on something constructive.
2. Do you honestly never begin to think, even for a moment, that if everyone disagrees with your interpretation of the evidence, and no one thinks that you have presented a valid argument of any kind, the problem might just be with you and not us? That we might actually be right, after all? Do you even consider this possibility? (If not, we're back at Q1.)
You folks are not the only ones I have presented my ideas to.
Every person I present these ideas to in person has been open to them. And I have presented to many.
You do not realize how very peculiar you folks are in the total population. How closed minded you are.
You really do not realize it.
"You do not realize how very peculiar you folks are in the total population."
Sadly, Anonymous, I suspect you are right there. You only need to look at the number of believers in Homeopathy, Young Earth Creationists, and other religious fundamentalists to see that the majority of people are willing to accept ideas without first asking for evidence or explanation.
I think you will find that we are not peculiar in the total scientific population or, even, the in the total University-educated population.
Truth is not determined by democracy, popularity or debate. If your ideas are sound, you should be able to defend them with evidence and a solid theoretical framework, not just empty words and empty insults.
By the way, you folks have actually contributed very little in fact.
But your questions do spur me to research the areas you bring up.
These subjects are fascinating. And every road of inquiry leads to the conclusion of the intelligence of Nature.
cabbagesofdoom has given the standard self-important, biased line.
His argument at first was that nobody agreed with me.
Then when he acknowledges that few agree with him, he changes his line.
But this is certainly not worth arguing about.
Anon: "These subjects are fascinating. And every road of inquiry leads to the conclusion of the intelligence of Nature."
And therein lies your problem. If you have decided where every road leads before you set off, why even bother? Science does not work like this. We see where the road takes us and then try to explain the journey, not pick the destination and then stubbornly refuse to be deflected. How you cannot see this, is beyond me. How you can then have the outrageous cheek to accuse us of this is truly mind-boggling.
You still haven't answered my questions though: (1) Why do you post here? (2) Are you not even willing to consider the possibility that you might be wrong?
Anon: "cabbagesofdoom has given the standard self-important, biased line.
His argument at first was that nobody agreed with me.
Then when he acknowledges that few agree with him, he changes his line.
But this is certainly not worth arguing about."
I beg to differ. I have not changed my line. Let me spell it out for you:
No one with any scientific training or understanding would agree with what you have presented in this forum.
Anyone who does agree with you on the basis of what you have presented here is a gullible fool.
If you can demonstrate where I have said otherwise, I will apologise. If not, I expect an apology.
Please do not extrapolate and put words in my mouth. It is rude.
PS. You've still not answered my questions. This is also a bit rude as I keep answering yours.
Just as a sidenote.
People have commented on the fact that I cut and paste. What I do is quote relevant material. And give the link address.
The folks here rarely do that. They present their opinions without any actual support.
For example, when Lou Jost (who generally I admire) posted his idea about the extent of physical reproductive isolation, occurring again and again he never quoted any source of support for that idea. If people were honest they would admit that they have never read anything about that idea taken to such an implausible extreme.
I give that as just one example.
I always admire and appreciate anyone who supports their thinking with actual links.
But people rarely do it.
No use in pointing out the rare occasion when someone has provided a link. I am speaking about the vast majority.
And people rarely accuse me of quote mining, because I am conscientious to paste substantial sections to give the context.
But this is also not worth arguing about.
It is still not clear whether people recognize the difference between speciation which is just a new species of the same type of creature on the one hand
and
the speciation of a new type of creature on the other hand.
Evolution theory cannot explain the latter type.
So evolutionists who think there is no need for the intelligence of Nature are fooling themselves. Evolution theory is not capable of explaining the speciation of new types of creatures.
When the same type of creature has a small modification from others of its type, it is not significant whether they can interbreed or not.
The issue is that they are still the same type of creature.
As a general rule a different type of creature is a different genus.
Two creatures of the same genus, whether they can interbreed or not are simply species subgroups.
To use the famous example, two finches that cannot interbreed are still finches.
This link shows the different ways of thinking about "species":
http://en.wikipedia.org/wiki/Species#Definitions_of_species
To truly get an idea of "evolution" you must focus on genera.
"If you have decided where every road leads before you set off, why even bother?"
I did not say that.
Quite the contrary.
@Socrates/Doug/Anus/Anonymous Every person I present these ideas to in person has been open to them. And I have presented to many.
That is a lie Socrates. A quick perusal of talkorigins shows that you flog the same dead horse there that you do here and that you have no interest in the exchange of ideas. It's all one way with you.
A quick sample of responses to your ideas:
Crap. If you knew the first thing about GRN's you would know that it is bottom-up. Read something by Davidson, Wolpert, Gilbert, Carroll etc before gobbing off.
We need a "reported for sheer unadulterated stupidity" button.
Tiel, you should know that doug (or Socrates as he styles himself) is a dickless weasel who'll endlessly pester you to spoon-feed him information he can't understand. That's his MO.
Moran are you actually committed to the idea of not having personal info disclosed on your blog or does that only apply to Rhett Daniels and not as a general principle?
As a general rule a different type of creature is a different genus.
Two creatures of the same genus, whether they can interbreed or not are simply species subgroups.
To use the famous example, two finches that cannot interbreed are still finches.
This link shows the different ways of thinking about "species":
http://en.wikipedia.org/wiki/Species#Definitions_of_species
To truly get an idea of "evolution" you must focus on genera.
As in all aspects of this subject it takes thought and analysis to see where to draw lines.
Anonymous said...on Wednesday, August 31, 2011 11:07:00 AM
(Lots of thing he said before. Fantasy that has been answered).
As a general rule a different type of creature is a different genus.
To truly get an idea of "evolution" you must focus on genera.
Genera don't come about by 'speciation of a new type of creature' due to 'the intelligence of Nature'.
For one thing, genera are constructs by taxonomists, for ease of filing species. For instance, the genus Drosophila might be split into the genera Drosophila and Sophophora. About all of the cats have been placed in the genus Felis at some time or other, and at the other extreme many cat species have been put into their own genus. Nobody can tell whether a paleontological genus and a neontological genus correspond.
For another thing, molecular studies show that a continuum of molecular distances between species, genera, families, the lot, all the unranked groupings included. There is no hiatus that can be construed as indicating a different process. Both the cats and Drosophila demonstrate that the genus does not correspond to a 'new type of creature'. In fact, looking through the mammals carefully, according to their phylogeny, it is fairly difficult to find 'a new type of creature'.
Reference material:
http://www.encyclopedia.com/topic/biological_species_concept.aspx#2-1O8:biologicalspeciesconcept-full
biological species concept
"The view that the species comprises populations (or groups of populations) that are reproductively isolated from each other, i.e. that species should always be biospecies. This has been mistakenly interpreted as implying that either they cannot interbreed, or that hybrids between them are sterile; but there are many reproductive isolating mechanisms. The concept was proposed by Ernst Mayr in the 1940s, but many biologists have come to regard it as too restrictive. For example, species that are not sister groups may interbreed in nature. Further, the professional taxonomist, usually working in a museum, must make (often unwarranted) judgements about whether two taxa might or might not be capable of interbreeding in nature. Other species concepts (the recognition, cohesion, and, especially, the phylogenetic species concepts) have come to be employed more and more in recent years."
http://www.encyclopedia.com/topic/phylogenetic_species_concept.aspx#2-1O8:phylogeneticspeciesconcpt-full
phylogenetic species concept
"The view that a species should be defined only by its diagnosibility; i.e. that it consists of a population with a unique set of features (preferably derived). This definition was proposed by Joel Cracraft in 1982 as a more workable alternative to the biological species concept, which implies knowledge of whether or not regular interbreeding occurs between populations."
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1990.tb00541.x/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+3+Sep+from+10-12+BST+for+monthly+maintenance
"Abstract— The goal of a phylogenetic species concept is to reveal the smallest units that are analysable by cladistic methods and interpretable as the result of phylogenctic history. We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character-based and pattern oriented. Evolutionary explanations of phylogenetic species are consistent with contemporary explanations of processes of speciation, but require only the assumption of nested hierarchical pattern. We discuss the compatibility of the phylogenetic species concept with various biological needs for species and justify its use at the exclusion of alternative species concepts."
So there is an alternative to the "biological species concept" (species definition based on interbreeding).
That alternative is the "phylogenetic species concept" which may be a more up to date concept.
Now I expect some sort of criticism of this, because the folks here are used to only one form of thinking - which is to object and strain mightily to find something to criticize, whether objecting makes sense or not.
Using the phylogenetic species concept in an analytic, thoughtful way could lead us to categorize different creatures that do not interbreed to be within the same species.
For example, two finches* that are both obviously finches could be considered as the same species, even if they could not interbreed.
The two (non-interbreeding) finches would be subgroups within the species.
*finch taxa
So there is an alternative to the "biological species concept" (species definition based on interbreeding).
That alternative is the "phylogenetic species concept" which may be a more up to date concept.
Now I expect some sort of criticism of this, because the folks here are used to only one form of thinking - which is to object and strain mightily to find something to criticize, whether objecting makes sense or not.
Granted I ignored most of the commentary yesterday as I was otherwise occupied, but as an evolutionary biologist why the hell would I criticise the Phylogenetic Species Concept? In fact, it's one that I am a rather large advocate for.
I even alluded to the fact, in one of my earlier comments, that the Biological Species concept, and the "rules" for different speciation scenarios are almost universally only applicable to animals, and even then they can be fuzzy. I believe ring species (which violate the strictest version of the biological species concept) have also been mentioned.
In fact there has been at least one comment (based on a quick scan) explicitly pointing out that species concepts are human constructs that model biological reality, they are not the reality itself.
Genera, and higher level taxonomic classifications are even more abstracted models reflecting this nested hierarchy.
Using the phylogenetic species concept in an analytic, thoughtful way could lead us to categorize different creatures that do not interbreed to be within the same species.
For example, two finches* that are both obviously finches could be considered as the same species, even if they could not interbreed.
The two (non-interbreeding) finches would be subgroups within the species.
*finch taxa
You seem to be under the illusion that under the phylogenetic species concept, what we call genera would then become what we call species.
In this assumption you would be incorrect.
Under the phylogenetic species concept we replace the somewhat ad-hoc delineation (in animals) of interbreeding populations as the criteria by which we split species by the also ad-hoc criteria of "sufficient genetic divergence". It all comes down to what we decide the relevant threshold is.
In some cases the phylogenetic species concept may lump together organisms that we now classify as two distinct species, in other cases sub-populations will be split off into their own species definition.
In fact we use some of these criteria already in animals when it is problematic to assess whether they meet the biological species definition but upon sequence analysis have clearly been diverging from one another for some time.
With the phylogenetic species concept we are on much stronger ground to analyze the material we have been discussing.
In fact we are actually getting closer to "kinds"!
Oh, oh. I can hear the warning bells already.
Everybody knows that talk of "kinds" is heresy.
There must be something wrong here.
I leave it to the folks here to explain (disdainfully I hope) why "kinds" is a COMPLETELY different thing!
"You seem to be under the illusion that under the phylogenetic species concept, what we call genera would then become what we call species.
In this assumption you would be incorrect."
I did not say that.
"You seem to be under the illusion that under the phylogenetic species concept, what we call genera would then become what we call species.
In this assumption you would be incorrect."
I did not say that.
Your previous comments about "kinds" at the very least implies something very similar. That under the phylogenetic species concept we would be getting towards something more similar to what are currently higher level taxonomic divisions.
It all depends on what somewhat arbitrary threshold of genetic divergence is decided on as being the demarcation point by which we classify species. In some cases it will lump together species into a single species, in others it will split them.
Anonymous changes the subject again. Weak strategy.
Could Anonymous stick to a subject? That is usual in a discussion.
Anonymous said on Wednesday, August 31, 2011 11:07:00 AM
.... the difference between speciation which is just a new species of the same type of creature on the one hand
and
the speciation of a new type of creature on the other hand.
Evolution theory cannot explain the latter type.
As a general rule a different type of creature is a different genus.
To truly get an idea of "evolution" you must focus on genera.
That kite didn't fly.
Now phylogenetic vs biogocial species concepts: nothing to do with the above. Just a new topic. Anonymous never is able to follow a line of thought, and always tries to get to a new topic to confuse people whatever he might be talinkg about.
The copying pasting of species concepts serves no use whatsoever.
Anon: "But your questions do spur me to research the areas you bring up... And every road of inquiry leads to the conclusion of the intelligence of Nature."
Me: "If you have decided where every road leads before you set off, why even bother?"
Anon: "I did not say that. Quite the contrary."
OK, Anonymous. Please explain how defining where "every road leads" [your words] before you "research the areas [we] bring up" [your words] is not deciding "where every road leads before you set off" [my words] ?
Can anyone help cabbagesofdoom?
He seems to have lost the ability to understand straightforward sentences and expects me to spoon feed his purposeful misunderstandings.
I have a great deal of experience dealing with individual people who purposefully misconceive the simplest things and then expect me to help them. I stopped doing that a long time ago.
Here is a clue - I did not say "before". Do people notice that? cabbagesofdoom added that.
That was sly.
heleen: "The copying pasting of species concepts serves no use whatsoever."
We did ask for a species definition waaaaaaay up thread. At least Anonymous has finally defined something. I'd call that progress! Now, if (s)he can just make the leap to understanding the definition...
I want to know what comes next, though. Nice to see we've made it to "kinds". (In the immortal words of Tim Minchin: "I feel like a rabbit caught in the headlights of vacuous crap.")
cabbagesofdoom, I see no reason to continue discussion with you.
You are rude and sly.
Anonymous, "where every road leads" clearly implies that the end of the road has not yet been reached, and yet you are stating where it leads. Hence, before you have got to the end, you have decided where it leads.
Did you mean to say "every road has lead to", which would imply that you are talking about past investigations and not the future ones that were the subject of that post?
Learn to write before criticising the comprehension of others.
People will notice that I never said "where every road leads".
Even though cabbagesofdoom put it in quote marks.
But this is enough wasting time on this slyness.
I apologise for being rude. It was born from frustration but that is not a sufficient excuse. I was not being sly, though, just honestly interpreting what you wrote as best I could given the context and the words.
Hi DG.
You posted about my:
"previous comments about "kinds"
I scanned the previous posts and noticed that I did not use the word "kinds".
Lou Jost used it a few times.
Apologies if I misplaced the quote mark. To remind, you, here was your original quote:
"But your questions do spur me to research the areas you bring up.
These subjects are fascinating. And every road of inquiry leads to the conclusion of the intelligence of Nature."
Anonymous, "every road of inquiry leads" clearly implies that the end of the road has not yet been reached, and yet you are stating where it leads. Hence, before you have got to the end, you have decided where it leads.
Did you mean to say "every road of inquiry has lead to", which would imply that you are talking about past investigations and not the future ones that were the subject of that post?
Learn to write before criticising the comprehension of others.
Note also how the meaning of my post was completely unchanged by my extra where. How sly of me!
Now, I expect an apology in return. But don't worry, I will still cease "discussion" with you, for you have still failed to answer any of my questions with anything other than rude accusations.
"Your previous comments* about "kinds" at the very least implies something very similar. That under the phylogenetic species concept we would be getting towards something more similar to what are currently higher level taxonomic divisions."
In some cases that may be, in other cases it may go the other way.
We need to look at each case.
*I made no previous comments using the word "kinds"
DG posted:
"It all depends on what somewhat arbitrary threshold of genetic divergence is decided on as being the demarcation point by which we classify species."
I suspect that what you refer to as arbitrary would line up pretty well with what most children would intuitively know. That is a tiger, that is a giraffe, that is a goat.
And in the case of, for example kinds of birds, I expect that my old bird book showing kinds of birds would line up with what you call "arbitrary threshold".
You are looking at this upside down.
NATURE sorts animals. We just recognize the sorting.
There will always be difficult cases but what I am saying is still correct.
I have posted twice an answer to the crucial misunderstanding articulated by jaxkayaker - but apparently this blog owner censors out from the 289 entries those that document the collapse of the half-a-Century hindrance of "Central Dogma". Submission for publication will be documented for the case that the blog is an instrument for ideology, entertainment and inflicting personal damages.
jaxkayaker said...
(my comment) "Now we know that proteins (e.g. methyl transferase) are capable of changing sequence information of DNA (e.g. the retrieval of DNA sequence information due to methylation)."
(jaxkayaker replied): Methylation of DNA bases does not change the sequence of DNA bases. Crick said that the central dogma (poor word choice on his part) forbade transfer of sequential information (i.e. residue to residue, in some ratio, not necessarily 1:1). Methylation doesn't do that.
==
My thesis is that while methylation does not change the formation of "sequence", making bases unreadable definitely alters "sequence information". (For the benefit of non-experts I used a simplistic metaphor of English that e.g. TAGGAGCAT, when two G-s rendered unreadable will reveal the info TAG A CAT. Information is not obvious from encrypted formation without the understanding how information is encoded. A sculpture emerges "by removing the excess stone" - information can likewise be revealed by rendering sequences unreadable by methylation.
No amount of papering over this fact will do, since it is crucial to developing cancer (see YouTube at min. 30 of "Is IT ready for the Dreaded DNA Data Deluge"). As shown, aberrant methylation, failing to cancel info supporting fractal iterative growth leads to uncontrolled (cancerous) growth.
This thread of close to 300 entries is interesting but millions if not hundreds of millions of people are dying of "junk DNA" diseases like cancer, and looking the other way will not help.
"My thesis is that while methylation does not change the formation of "sequence", making bases unreadable definitely alters "sequence information". (For the benefit of non-experts I used a simplistic metaphor of English that e.g. TAGGAGCAT, when two G-s rendered unreadable will reveal the info TAG A CAT."
I'm afraid that this isn't how methylation works. It alters the chromatin structure (packaging) of the DNA and thus makes large stretches "silent". It does not simply "silence" the individual bases that are methylated. In your metaphor, the whole page is stapled shut: nothing gets read.
cabbagesofdoom did exactly what I expected; taking my "simplistic metaphor using the English language" way too literally to show that info from encrypted messages can be revealed by silencing parts of sequence. At the same time, I got cabbagesofdoom acknowledge that "It alters the chromatin structure (packaging) of the DNA and thus makes large stretches "silent"".
Who would now deny that protein-induced methylation alters "sequence information" (wherever "sequence information" is properly defined, as in The Principle of Recursive Genome Function)?
Anonymous wrote at 3:15 pm:
With the phylogenetic species concept we are on much stronger ground to analyze the material we have been discussing.
In fact we are actually getting closer to "kinds"!
Oh, oh. I can hear the warning bells already.
Everybody knows that talk of "kinds" is heresy.
There must be something wrong here.
I leave it to the folks here to explain (disdainfully I hope) why "kinds" is a COMPLETELY different thing!
Anonymous wrote at 4:29 pm:
Hi DG.
You posted about my:
"previous comments about "kinds"
I scanned the previous posts and noticed that I did not use the word "kinds".
Lou Jost used it a few times.
Anonymous wrote at 4:35 pm:
"Your previous comments* about "kinds" at the very least implies something very similar. That under the phylogenetic species concept we would be getting towards something more similar to what are currently higher level taxonomic divisions."
In some cases that may be, in other cases it may go the other way.
We need to look at each case.
*I made no previous comments using the word "kinds"
Was this some other Anonymous at 3:15 pm, or were your comments at 4:29 and 4:35 pm incorrect?
Anonymous writes:
I suspect that what you refer to as arbitrary would line up pretty well with what most children would intuitively know. That is a tiger, that is a giraffe, that is a goat.
That is a chihuahua, that is a wolf, that is a coyote. Oh, wait. Two of the three are the same species. I'm sure any child would be able to recognize which two are the same species, right?
Shit, it's like throwing marshmallows at an elephant! Do organisms give a damn about our species concept? Genes can only flow about a sexual population where real interbreeding takes place. Where it does not, they cannot. End of story. And that matters, crucially.
Once genetic isolation is in place (specifically, repeated failure at any stage up to and including gamete formation in the next generation), the stage is set for progressive divergence through things that we choose to label as higher hierarchic groupings, with further branching on the way. You may choose to ponder why those groupings are hierarchic, but I have no confidence that will strike you as meaningful.
You remind me of a contestant on X Factor or Pop (American) Idol, convinced you can sing like a bird. While we are all differently abled in our ability to carry a tune, most people have some awareness of their limitations.
And Pellionisz, methylation is no more passage of sequential information from protein to DNA than is the operation of a genetic switch that prevents transcription. Many enzymes have elements of the transcription/translation system as their substrate, and that has never been regarded as invalidating the dogma.
Some (most?) of what is called speciation is actually adaptation leading to new subspecies within a species. For example, finches with slightly different beaks are mis-categorized as different species based on the artificial basis of non-interbreeding.
To use the famous finch example:
They may be different but they are still finches.
In other words, it is not actually speciation in the phylogenetic species concept sense.
It is just misleading and unhelpful to call them different species.
Perhaps it is just old fashioned as the article implied.
No. no. no! It's not what we call them that counts. It's what actually happens, out there in the wild. Genes ultimately flow through meiotic recombination, which requires sex. No recombination, no gene flow. If gene flow is stemmed, nothing is shared, and genes cannot get from one to the other. Then, there is nothing to prevent genetic divergence, indefinitely. Nothing.
It's not what we call them that counts. It's what actually happens, out there in the wild. Genes ultimately flow through meiotic recombination, which requires sex. No recombination, no gene flow. If gene flow is stemmed, nothing is shared, and genes cannot get from one SUBSPECIES to the other.
I have added the word "subspecies" to your post.
Does that work for you?
Anonymous writes:
For example, finches with slightly different beaks are mis-categorized as different species based on the artificial basis of non-interbreeding.
To use the famous finch example:
They may be different but they are still finches.
In other words, it is not actually speciation in the phylogenetic species concept sense.
Since you're sufficiently expert on the subject to make these assertions, please provide us the differences in the results of peer-reviewed academic classifications of finches using the biological species concept on the one hand, and the phylogenetic species concept on the other.
Lest anyone think Socrates/Anonymous is being treated harshly here, a little constructive criticism sent his way at talkrational (apparently Socrates thinks birds are descended from pterosaurs, amongst other delusions):
And by the way, fuckhead: starting from "scratch" would mean her evidence doesn't support placing hadrosaurs anywhere in the tree of life at all.
No. Read the fucking paper, moron. She agrees that birds are descended from maniraptors, as the morphological evidence supports.
The words in red are, of course, "Socrates's" invention and appear nowhere in the original. Birds are closer to pterosaurs than to crocodiles, not dinosaurs.
This last one is interesting, apparently Socrates was diddling his sources. Shame on you Socrates.
This is far from the truth - as usual Socrates is taking quotes out of context and misusing them to cast Dave Hone in a negative light. Socrates is trying to make out it was some sort of epic battle of wits and he got Dave to eventually admit defeat. Nothing could be further from the truth.
Colour me surprised.
If nothing else, Socrates is the most masochistic troll I've had the pleasure of seeing in action. Constructive criticism rolls off his back and abuse just keeps him coming back for more.
I spent a few minutes looking at various threads at talkrational and there is not one that Socrates got involved in and did not derail.
Why not let the great man speak for himself:
I did not mention it because I am banned there and cannot see it. Your innuendo is that I am lying. I have warned you about that. This is one more warning.
I'm shocked, simply shocked that Socrates may have indulged in this bad behaviour on other sites to the point where he was banned.
Add a dollop of paranoia and we have a well rounded wingnut.
Anonymous, since you feel sufficiently expert on the subject of finches and the phylogenetic species concept that you believe finches should not be separate species, would you please give us your scientific reasons for disagreeing with the conclusions of all the scientists in the academic discussion of classification of Darwin's finches at the following page:
http://www.museum.lsu.edu/~remsen/SACCprop367.html
Most of these scientists feel, on the basis of the phylogenetic species concept and other species concepts, that there should be an *additional* species of finch. None of them argues for *fewer* species.
http://www.encyclopedia.com/topic/phylogenetic_species_concept.aspx#2-1O8:phylogeneticspeciesconcpt-full
phylogenetic species concept
"The view that a species should be defined only by its diagnosibility; i.e. that it consists of a population with a unique set of features (preferably derived)".
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1990.tb00541.x/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+3+Sep+from+10-12+BST+for+monthly+maintenance
"We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character-based and pattern oriented.
I think we've been had, people. Socrates is a sophisticated troll. Throw a few plausible arguments around and fish for responses, then orchestrate them into some wild cacophony for fun. He's a virus. A good argument for reintroducing comment moderation, sadly.
steve oberski and Allan Miller are clearly trolls.
I look forward to moderation so their trolling can be monitored.
They routinely post inflammatory,extraneous, or off-topic messages in an online community, such as an online discussion forum, chat room, or blog, with the primary intent of provoking readers into an emotional response.
And that Moran allows them to post personal information about others is beyond outrageous. Especially after Moran alerted us to Rhett Daniels.
There is a pattern.
In the face of ideas that they disagree with, the discussion degenerates into insults and personal attacks leading to the disclosure of personal information and threats.
This is all based simply on someone posting ideas they disagree with.
Sad that just the posting of different ideas brings forth such hatred.
This is what has been correctly condemned in the case of Rhett Daniels.
I ask Moran once again to put a halt to this disclosure of personal information.
Is this a blog for the discussion of ideas (which people can agree or disagree with) or an opportunity for people to vent their hatred?
I posted:
"Sure, subgroups of a larger group can get spread out. At that point you have separated groups of the same type of creature. But you have no greater likelihood that the split-off group will evolve into a different type of creature than you had originally. Perhaps less, because as Moran told us, groups (eg. subgroups) less than 1,000 will likely go extinct.
The original problem is unchanged."
I hope that someone will speak to this seriously because it actually shows how completely superfluous the physical reproductive isolation argument is.
After physical reproductive isolation and even the appearance of subgroups (if that even occurs) we are no closed to a new species.
And certainly no closer to a new type of creature as one would associate with a new genera.
@Anonymous
If you are sincere, then I sincerely apologise for any offence. Everybody is free to engage with you if they are interested enough to do so.
Just ignore me.
http://en.wikipedia.org/wiki/Allopatric_speciation
"When populations become genetically isolated, heritable variations may accumulate so that they become different from the parental population. Given sufficient time, these variations may lead to reproductive isolation.
Portions of a populations that exist along the edges of the parent population's geographic territory have higher likelihood of developing reproductive isolation. Such peripheral populations are likely to possess genes that are different from the parental population. After isolation, the founding population is less likely to represent the gene pool of the parent population. In addition, peripheral isolates are likely to represent a small number of individuals, meaning their gene pool is more susceptible to the effects of genetic drift (random chance). Furthermore, it is likely that the peripheral population will inhabit an environment different from its ancestral gene pool, likely causing it to be subjected to different selective pressures as it colonizes new areas. The outer periphery of a population's habitat tends to be extreme; hence, the reason range expansion is kept in check. For most peripheral isolates, it is more likely that they die off rather than survive and speciate.
it is more likely that they die off rather than survive and speciate.
This whole discussion of physical reproductive isolation is a complete red herring.
What Pagel brought to light in his study was not instances of physical reproductive isolation leading to speciation, but instances of large genetic reorganizations (saltations) generating new species.
Or as he put it:
"It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak."
@Anon
Lets talk about a few of your misconceptions. Firstly we have already addressed your problems with physical isolation three times, from three distinct perspectives at Tuesday, August 30, 2011, 7:42:00 PM,August 30, 2011, 7:57:00 PM,and Wednesday, August 31, 2011 4:40:00 AM. Secondly Pagel explicitly talks about physical isolation barriers within the paper. "We suppose there are many potential causes of speciation, including environmental and behavioural changes, purely physical factors such as the uplifting of a mountain range that divides two populations, or genetic and genomic changes." Thirdly no one here as far as I'm am aware has threatened you in anyway, the point of the EpiRen story was a)simply to inform people of how much of a cad Rhett was and b)to illustrate why people may choose to keep personal information off the internet. It is not an excuse for you to whine that people here now know who you are because you disclosed your own damn information in the first place.
Anonymous gets less and less consistent in the discussion on speciation, and more and more parasitizing on people's politeness and tendency to explain things they are interested in. It is simply impossible to have any rational discussion with Anonymous.
Anonymous said... on Wednesday, August 31, 2011 11:37:00 PM
In the face of ideas that they disagree with, the discussion degenerates into insults and personal attacks leading to the disclosure of personal information and threats.
Anonymous is certainly guilty of insulting people. Nobody has threatened him. It is a fact, not an insult, that Anonymous is abysmally ignorant of biology.
This is all based simply on someone posting ideas they disagree with.
Sad that just the posting of different ideas brings forth such hatred.
Is this a blog for the discussion of ideas (which people can agree or disagree with) or an opportunity for people to vent their hatred?
The venting of hatred is mostly by Anonymous.
If Anonymous wants to discuss ideas, he should listen to what others have to say. Anonymous never does. Anonymous never sticks to a line of argument if he has no answer, but just throws out the next topic.
Allan Miller said... on Wednesday, August 31, 2011 11:12:00 PM
I think we've been had, people. Socrates is a sophisticated troll. Throw a few plausible arguments around and fish for responses, then orchestrate them into some wild cacophony for fun. He's a virus. A good argument for reintroducing comment moderation, sadly.
I agree with Allan Miller that Anonymous provides a good argument of reintroducing comment moderation, but I don't think Anonymous does it for fun. I thing he's serious. More's the pity.
Pellionisz said...
I have posted twice an answer to the crucial misunderstanding articulated by jaxkayaker - but apparently this blog owner censors out from the 289 entries those that document the collapse of the half-a-Century hindrance of "Central Dogma". Submission for publication will be documented for the case that the blog is an instrument for ideology, entertainment and inflicting personal damages.
Your paranoia is showing (again). Every time you accuse me of censoring comments you've been proved wrong.
You know very well that I allow everything on this blog except spam that advertises a commercial product. You know very well that I even allow well-known kooks to post comments.
Why do you persist in making up paranoid stories about censorship?
Oh, I know, it's because you're a kook. That's one of the symptoms of kookiness.
anonymous the IDiot asks,
Moran are you actually committed to the idea of not having personal info disclosed on your blog or does that only apply to Rhett Daniels and not as a general principle?
I've made no such commitment.
I'm opposed to people who try to harass their blog opponents in the real world. This includes making threats and sending email messages to friends, family, and employers.
I'm guessing that you are referring to someone who says you are Doug Dobney from Peterborough, Ontario, Canada. I have no idea whether that's true or not.
Is it?
You have posted over one hundred comments on my blog as "anonymous." That's very confusing since there are many others who comment anonymously. If your name really is Doug Dobney then why not just use your name?
I'm out too. Things have gone full circle, possibly twice, and my curiosity has diminished to the point that I can't bear to see the same murdering of biological principles and blind refusal to accept reality any more.
A few parting thoughts, though:
@Allan Miller, Jud, heleen, DG et al. - hope to bump into you again in a discussion that is actually about science! Sorry for indulging the fantasies longer than was healthy. (Socrates must be spinning in his grave.)
@Larry Moran: very sorry for indulging the fantasies longer than was healthy. It's a shame to see the comment thread of an interesting post deteriorate to quite the extent that it did.
@Pellionisz: "As shown, aberrant methylation ... leads to uncontrolled (cancerous) growth." The good news for you is that this can still be true even if you accept the proven relationship between methylation and gene expression. There is no need to re-define "sequence information" (or, for that matter, introduce "fractal iterative growth"). Just be aware that plenty of well-known point mutations is protein-coding genes can also de-regulate the cell cycle and cause (or contribute to the cause of) cancer.
@Pellionisz: I also owe you an apology as, earlier in the thread, I got you confused with Anonymous. Sorry about that. (And well done for at least staying on topic.)
@Anonymous: (a) Knowing you post in another forum does not constitute dangerous "personal information". I learnt nothing personal about you that your posts here had not already revealed; (b) If you really are serious, and don't see the problem with your manner of engagement, please get some help. Perhaps get a "critical friend" to read your posts and see how they appear to others. (c) For the last time, the Pagel paper had nothing to do with saltation or large genetic changes - re-read my quotes from the paper earlier in the thread. (d) a "unique combination of character states" is usually based on molecular data these days. What Jud and others have kindly told you is perfectly true. (e) If you feel you have lots of new ideas and are misunderstood by all here, I suggest going somewhere else or writing a book. But mainly, going somewhere else.
cabbagesofdoom writes:
@Allan Miller, Jud, heleen, DG et al. - hope to bump into you again in a discussion that is actually about science!
Yep, feeling's mutual.
To no one's surprise, Anonymous would not respond to my invitation to come to grips with the application of the phylogenetic species concept to the very example he used, finches.
So closes yet another chapter of Anonymous attempting to redefine scientific terms in some ridiculous way of his own.
As I and others have alluded to previously, it's quite sad. If Anonymous expended half the energy on study as he does on making stuff up for a totally non-receptive audience, there would be absolute glories of scientific information open to him.
I'll see if I can resist the temptation to further clutter this thread, though I'm reasonably sure Anonymous will make further attempts at eliciting responses from someone, anyone, to fulfill whatever need it is that keeps him posting here.
@Allan Miller, Jud, heleen, DG et al. - hope to bump into you again in a discussion that is actually about science!
Cheers! Despite the negatives, I learnt something, and enjoy trying to understand my own position by articulating it to others. I do feel uncomfortable about some things - I have been in pretty much the same position as Anon, trying to articulate a left-field (but non-mystical!) position in the face of universal online hostility. It prompted me to try and understand why I was triggering such reactions just by straying outside my specialism. I bought a couple of relevant textbooks and tried to get to grips with the basics a bit more.
So if I have overdone it at all, Anon, I do apologise. Biology is a fascinating topic, and it all fits together with a very satisfying 'clunk'. I'm off to chuck marshmallows at an elephant! :0)
Dr. Moran I am surprised you are so short-sited about the disclosing of personal information.
When a person's personal information is disclosed, the individual can begin to get hatred emails and threatening telephone calls.
These threats can be against one's family.
I have even received threats that the hater will come to my home and kill me and my family.
You greatly underestimate the extent of how far people filled with hatred will go.
The Rhett Daniels case has taught you nothing.
And all because I post ideas that people disagree with.
Dr. Moran, how would you feel about receiving death threats against your grand daughter.
Does that help you to understand this better?
http://en.wikipedia.org/wiki/Allopatric_speciation
"When populations become genetically isolated, heritable variations may accumulate so that they become different from the parental population. Given sufficient time, these variations may lead to reproductive isolation.
Portions of a populations that exist along the edges of the parent population's geographic territory have higher likelihood of developing reproductive isolation. Such peripheral populations are likely to possess genes that are different from the parental population. After isolation, the founding population is less likely to represent the gene pool of the parent population. In addition, peripheral isolates are likely to represent a small number of individuals, meaning their gene pool is more susceptible to the effects of genetic drift (random chance). Furthermore, it is likely that the peripheral population will inhabit an environment different from its ancestral gene pool, likely causing it to be subjected to different selective pressures as it colonizes new areas. The outer periphery of a population's habitat tends to be extreme; hence, the reason range expansion is kept in check. For most peripheral isolates, it is more likely that they die off rather than survive and speciate.
it is more likely that they die off rather than survive and speciate.
This whole discussion of physical reproductive isolation is a complete red herring.
What Pagel brought to light in his study was not instances of physical reproductive isolation leading to speciation, but instances of large genetic reorganizations (saltations) generating new species.
Or as he put it:
"It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak."
That saltations could be the explanation of the origin of new species is for some reason a frightening idea to evolutionists.
They go to any length, including personal attack to avoid having to face up to the IDEA. And analyse it objectively.
The state of our knowledge has advanced so far that we now know about the tools that the intelligence of Nature can use in the large genetic reorganizations (ie. the genetic tookit etc).
http://en.wikipedia.org/wiki/Evolutionary_developmental_biology#The_developmental-genetic_toolkit
"The developmental-genetic toolkit consists of a small fraction of the genes in an organism's genome whose products control its development. These genes are highly conserved among Phyla. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. The majority of toolkit genes are components of signaling pathways, and encode for the production of transcription factors, cell adhesion proteins, cell surface receptor proteins, and secreted morphogens, all of these participate in defining the fate of undifferentiated cells, generating spatial and temporal patterns, which in turn form the body plan of the organism. Among the most important of the toolkit genes are those of the Hox gene cluster, or complex. Hox genes, transcription factors containing the more broadly distributed homeobox protein-binding DNA motif, function in patterning the body axis. Thus, by combinatorial specifying the identity of particular body regions, Hox genes determine where limbs and other body segments will grow in a developing embryo or larva. A paragon of a toolbox gene is Pax6/eyeless, which controls eye formation in all animals. It has been found to produce eyes in mice and Drosophila, even if mouse Pax6/eyeless was expressed in Drosophila."
We see all the evidence. Shapiro has demonstrated the mechanisms and many other researchers are studying the genetic toolkit.
And Pagel's data shows the saltations.
Here is a helpful link.
http://en.wikipedia.org/wiki/Facilitated_variation
Presumably people here are not familiar with all the thinking and study that has been done in the area I am talking about.
I would guess, Anon, that many of us commenting in this endless, now severely off-topic thread, are far more aware of the scientific research that has been (and is being) conducted in these areas than you are.
Many of the core concepts have been explored in this very blog. Dr. Moran likes to point out quite commonly that the overly narrow "traditional Darwinian" interpretations and explanations of evolution are rarely the actual views held by most in the field. That is especially true in my experience within molecular evolution.
I have attended many talks (at SMBE, Evolution, and Protistology conferences), and read many papers that cover areas like facilitated variation. Ideas like evolvability, evolution of interaction and regulatory networks, etc are hot areas of study in evolutionary biology, particularly within evo-devo.
DG, why did you not mention "facilitated evolution" until I brought it up?
Are you an objective searcher for the truth? Or just an apologist for current evolution theory thinking?
Do you see that "facilitated evolution" is quite similar to the ideas I have been presenting?
I didn't bring it up because I didn't particularly see the need to try and get into how evolutionary biology isn't limited to point mutations and natural selection.
And no, it doesn't support whatever your current poorly worded mangled hypothesis seems to be. Neither Facilitated Evolution nor Pagel's work support old-school Saltationism (which generally put forth sudden immense changes from one generation to the next) or sudden diversification on the level of one genera to another.
I, and other commentators, have been trying unsuccessfully to explain exactly why so many fundamental pieces of information you bring up are so badly misunderstood by you.
Its like you read short wikipedia articles, pass them through a selective filter, and think you grasp the fundamental concepts. Its a perfect example of the Dunning-Kruger effect in action.
Anonymous, how do you know that you are an objective searcher of the truth?
Ah, the old "Dunning-Kruger" slur.
Each time someone posts that slur, they think they are new and original.
It is just another of those lazy insults, that people are forced to use when they cannot constructively present their own ideas.
Your posts are generally good DG. I was hoping for better from you.
It is a shame you cannot acknowledge that "facilitated evolution" is quite similar to the ideas I have been presenting.
I simply build on the biological evidence and modern thinking and ask "Who/what is doing the "facilitating"?
http://en.wikipedia.org/wiki/Facilitated_variation
"They explain how the individual organism can change from a passive target of natural selection, to a central player in the 3-billion-year history of evolution."
As soon as we are talking about the ORGANISM as an ACTIVE player (rather than a passive target) we are without doubt entering into the area of the intelligence of Nature.
Anonymous asked how I knew I was an objective searcher for the truth.
I suggest to you that you read the form of the posts I have posted. They present actual quotes. I try to present the ideas in as simple and clear language as I can. I approach the subject from as many different angles as I can.
Also I do not hide data or make sly misquotes.
I go where the data leads us.
"I go where the data leads us."
But data – any data – must be interpreted. How do you know you are interpreting it objectively?
By what method did you completely free yourself of all your biases? Does this objectivity of yours extend into all other domains of thought, or are you just unbiased when discussing evolutionary biology, a field you are not a practitioner of?
Anonymous, I do not feel the need to answer all your questions.
Perhaps you could pose them to the others here about their objectivity. And also analyze the nature of their posts.
Have you followed the line of reasoning I have been presenting? What can you contribute?
Do you see a similarity between "facilitated evolution" and the ideas I have been presenting?
I should have said "facilitated variation".
To be precise "facilitated phenotypic variation".
Who/what is doing the facilitation?
steve oberski said...
"... I visited the Pellionisz web site .... I'm not competent to comment on the science aspect...
I appreciate the fact that Pellionisz sequestered himself away for 15 years before gifting the world with his paradigm shattering discoveries, but I wonder if he should have waited another 15 years or so."
History records that the obsolete "Central Dogma" and "Junk DNA" axioms got genomics sequestered by the old establishment into a half-of-a-Century setback - and those with vested interest in the old school would like at least to pretend (not for further 15 years but as long as they are alive) that their house of card has not collapsed. It has. Links to The Principle of Recursive Genome Function, its Cold Spring Harbor Lab presentation, popularization in YouTube as well a the seminal fractal recursion paper in 1989 are all available for a click - but is admitted that for those not competent to comment on the science aspect paradigm shifts are as meaningless as maintaining a Geo-centric world view obsolete for 300 years. Meanwhile, millions if not hundreds of millions of people are dying of "Junk DNA diseases" - not only those competent in science, but also those who are not.
steve oberski said...
"... I visited the Pellionisz web site .... I'm not competent to comment on the science aspect...
I appreciate the fact that Pellionisz sequestered himself away for 15 years before gifting the world with his paradigm shattering discoveries, but I wonder if he should have waited another 15 years or so."
History records that the obsolete "Central Dogma" and "Junk DNA" axioms got genomics sequestered by the old establishment into a half-of-a-Century setback - and those with vested interest in the old school would like at least to pretend (not for further 15 years but as long as they are alive) that their house of card has not collapsed. It has. Links to The Principle of Recursive Genome Function, its Cold Spring Harbor Lab presentation, popularization in YouTube as well a the seminal fractal recursion paper in 1989 are all available for a click - but is admitted that for those not competent to comment on the science aspect paradigm shifts are as meaningless as maintaining a Geo-centric world view obsolete for 300 years. Meanwhile, millions if not hundreds of millions of people are dying of "Junk DNA diseases" - not only those competent in science, but also those who are not.
Anon: Again I would say: go and read the actual scientific papers on facilitated variation, and some basic biology texts. Stop relying on wikipedia articles as the source of all information, and taking figurative/descriptive language a little too far in terms of the biological reality.
From the abstract of the 2007 Gerhart and Kirschner paper:
This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitatedotypic variation.
It is the properties of these core processes that do the facilitating in facilitated variation. Not some sort of guiding intelligence with some sort of intent.
Anonymous said...
Anonymous, I do not feel the need to answer all your questions.
Perhaps you could pose them to the others here about their objectivity. And also analyze the nature of their posts.
Have you followed the line of reasoning I have been presenting? What can you contribute?
Do you see a similarity between "facilitated evolution" and the ideas I have been presenting?
On the contrary, I do feel the need to doubt all your questions. Given that the line of reasoning Anonymous has been presenting is impossible to follow, Anonymous has not contributed anything. Perhaps Anonymous has no other desire than to get evolutionists as angry as possible?
There is no similarity between "facilitated evolution" and the ideas Anonymous has been presenting. Anonymous cannot understand Wikipedia: that is the problem with Anonymous.
Anonymous could have read the book, but that is seemingly too much trouble to Anonymous.
Anonymous said...
I should have said "facilitated variation".
To be precise "facilitated genotypic variation".
Who/what is doing the facilitation?
The intelligence of Nature.
http://en.wikipedia.org/wiki/Facilitated_variation
"In the classical Darwinian view, a large number of successive mutations, each selected for its usefulness to the survival of the organism, is required to produce novel structures such as wings, limbs, or the brain. Alternatively, facilitated variation asserts that the physiological adaptability of core processes and properties such as weak linkage and exploratory processes enable proteins, cells, and body structures to interact in numerous ways that can lead to the creation of novelty with a limited number of genes, and a limited number of mutations [changes].
Therefore, the role of mutations [changes*] is often to change how, where, and when the genes are expressed during the development of the embryo and adult."
*These changes are directed by the intelligence of Nature.
http://en.wikipedia.org/wiki/Facilitated_variation
"In the classical Darwinian view, a large number of successive mutations, each selected for its usefulness to the survival of the organism, is required to produce novel structures such as wings, limbs, or the brain. Alternatively, facilitated variation asserts that the physiological adaptability of core processes and properties such as weak linkage and exploratory processes enable proteins, cells, and body structures to interact in numerous ways that can lead to the creation of novelty with a limited number of genes, and a limited number of mutations [changes].
Therefore, the role of mutations [changes*] is often to change how, where, and when the genes are expressed during the development of the embryo and adult."
Consider the fact that novelty can be created "with a limited number of genes, and a limited number of mutations [changes]".
This means that salations are eminently feasible.
Is there anyone who disputes that?
If so, please explain your thinking.
While people consider what criticisms they can proffer I will continue.
Now that we see that saltations are eminently feasible, we can see that all that talk about physical reproductive isolation was just a dead end.
That sort of "explanation" is based on old thinking. On an old understanding of the structure and the dynamics of the genome.
With the current understanding that novelty can be created "with a limited number of genes, and a limited number of mutations [changes]" we see that all the evidence points to saltations.
The only question remaining is what triggers and controls those saltations, which bring into being new species? We know it is not adaptation to the environment.
Now that we see that saltations are eminently feasible, we can also look at specific examples.
Advanced pterosaurs developed into primitive dromaeosaurids. There are only advanced pterosaur fossils and primitive dromaeosaurid fossils. There are no transitional fossils. One developed directly into the other.
Is there anyone who will acknowledge a similarity between "facilitated evolution" and these ideas I am presenting? If not, please explain your thinking.
Well there is another "Anonymous" here posting.
Sounds like a person I have been getting hate emails from.
At my blog "http://pterosaurnet.blogspot.com/2011/07/senter-strikes-again.html#comments" I emphatically state that pterosaurs developed into dromaeosaurs with no intermediates. Do not be fooled by this other "Anonymous" who claims I believe pterosaurs developed into dromaeosaurs with no intermediates.
Who/what is "Intelligence of Nature?" What is motivation? How/why do they make saltations? Why speciation if no adaption? Why extinction? Do you have examples of genotypic saltation you mention and how they caused speciation?
@DG
Thus, we call it a theory of facilitatedotypic variation.
I sure hope that's a typo - I can't even say it!
Anonymous said...
At my blog "http://pterosaurnet.blogspot.com/2011/07/senter-strikes-again.html#comments" I emphatically state that pterosaurs developed into dromaeosaurs with no intermediates. Do not be fooled by this other "Anonymous" who claims I believe pterosaurs developed into dromaeosaurs with no intermediates.
Quite so. This was too hilarious to let it pass.
I don't know which is sadder, that Anonymous is arguing with itself and loosing or that it just can't stop it's reflexive, lizard brain controlled copy and pasting.
Thanks for pointing out that site:
http://pterosaurnet.blogspot.com/
On there it says that:
"The results of this study indicate that transitional fossils linking at least four major dinosaurian groups [Maniraptora is one of them] to the rest of Dinosauria are yet to be found."
I think this is the first time an evolutionist has told the simple truth. There are no transitional fossils between actual dinosaurs (such as Compsognathus and Tyrannosaurus) and Maniraptors."
http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02349.x/abstract
That sounds significant.
From an earlier post:
"Why speciation if no adaption?"
What do you mean by that?
Now that we see that saltations are eminently feasible, we can see that all that talk about physical reproductive isolation was just a dead end.
That sort of "explanation" is based on old thinking. On an old understanding of the structure and the dynamics of the genome.
With the current understanding that novelty can be created "with a limited number of genes, and a limited number of mutations [changes]" we see that all the evidence points to saltations.
http://en.wikipedia.org/wiki/Allopatric_speciation
"Furthermore, it is likely that the peripheral population will inhabit an environment different from its ancestral gene pool, likely causing it to be subjected to different selective pressures as it colonizes new areas. The outer periphery of a population's habitat tends to be extreme; hence, the reason range expansion is kept in check. For most peripheral isolates, it is more likely that they die off rather than survive and speciate."
Two significant points:
"The outer periphery of a population's habitat tends to be extreme; hence, the reason range expansion is kept in check."
and
"For most peripheral isolates, it is more likely that they die off rather than survive and speciate.".
It is not a good idea to base a lot on the supposed effect of purported physical (geographic) reproductive isolation.
Another problem that prevents people from accepting the feasibility of the massive single-generation saltational changes I am proposing is misinterpretation of the fossil evidence.
As I argued here: "http://talkrational.org/showthread.php?p=1509036#post1509036" ichthyosaurs developed into mosasaurs which then developed into whales. There were no intermediate stages, the changes were saltational and occurred within a single generation in each case. Only misinterpretation of the fossil evidence prevents recognition of this relationship.
The explanatory power of directed saltation through the intelligence of nature is undeniable. Only adherence to dogmatic Darwinism prevents wider acceptance of the ideas I am presenting.
There is a poster here who is pretending to be me and posting corruptions of the ideas I am presenting - pretty desperate to deal with the ideas I am presenting by corrupting them.
I suspect this is the person who has already gone to the extent of sending me hate emails.
This individual is desperate.
By "why speciation if no adaptation", I mean why have different species if they are not adapting to different things? What is the motivation of Nature to speciate? Who/what is the "Intelligence of Nature?" How/why do they make saltations? Why does extinction happen? Do you have examples of genotypic saltation you mention and how they caused speciation? Is there molecular evidence?
Anonymous posted:
"By "why speciation if no adaptation", I mean why have different species if they are not adapting to different things?"
I do not understand what you are getting at. I have already talked about where adaptation fits into the picture.
I can't find anything about a role for adaptation, only "saltation" and the "Intelligence of Nature". But then you have many posts. Please remind me and answer my other questions - what is this intelligence, what is its motivation, how do extinctions fit in etc. You have not touched on any of these important issues with your theory.
By the way, if you post as "Anonymous", you have no identity for someone to try and steal, so do not complain if others post contradictory stuff also under "Anonymous". If you want to "own" your ideas, use a name instead. (I have no ideas to own here, I just want to understand yours.)
Hugs and kisses, not-you-and-not-them-either-Anonymous.
Anonymous posted:
"so do not complain if others post contradictory stuff also under "Anonymous".
It is dishonest for someone to take my posts and add their own misleading additions to it and pretend to be me. It is a purposeful attempt to discredit my ideas.
If you cannot see that, then why would I continue discussion with you?
Do you think I am falling for this hugs and kisses stuff?
To Lou Jost, Jud, Allan Miller, cabbagesofdoom, Boojum, steve oberski, heleen, -DG and others I would like to say that I have read your posts and realize how completely moronic and idiotic my ramblings about species, saltation, and the intelligence of Nature were and apologize for wasting your time.
I also apologize to Pagel for completely misrepresenting his paper.
I have adjusted my medication and am feeling much better now.
Please feel free to visit me on my web site http://socratesisdougdobney.blogspot.com/
Doug Dobney
There is nothing to fall for. I simply want to understand your theory. At present it makes no sense to me because of the undisclosed details I have asked for. If you do not wish to explain your theory, that is your decision, of course.
The Anonymous poster pretending to be me has now hit the bottom of the barrel. I wondered when it would come to this.
This is the inevitable result of Moran not protecting personal information.
If people wish to consider me anyone they wish, then I have no control of that.
But notice that my focus is on the interesting biological subjects and not personal attacks.
It would be reasonable to conclude there is something quite wrong with this hatred-filled poster.
This is the sort of damage that Moran has opened the door to.
There is nothing that can be done with someone like the disturbed poster. But Moran should know better.
It will be very interesting to see if anyone here will criticize the actions of this disturbed, hater in our midst.
The Anonymous poster pretending to be me was actually me.
Don't be deceived by those other hate filled posters pretending to be me.
Moran has opened the flood gates for disturbed haters in our (or is that my ?) midst.
Coming back to the topic at hand:
Now that we see that saltations are eminently feasible, we can see that all that talk about physical reproductive isolation was just a dead end.
That sort of "explanation" is based on old thinking. On an old understanding of the structure and the dynamics of the genome.
With the current understanding that novelty can be created "with a limited number of genes, and a limited number of mutations [changes]" we see that all the evidence points to saltations.
The new understanding of the genome changes everything. It seems that the ramification of this new knowledge has not yet affected the rest of evolution theory thinking.
It will probably take time.
These are my exact words, from my blog here: "http://pterosaurnet.blogspot.com/2011/07/senter-strikes-again.html#comments"
"Advanced pterosaurs developed into primitive dromaeosaurids. There are only advanced pterosaur fossils and primitive dromaeosaurid fossils. You will notice that I have posted many posts showing that advanced preosaurs are already almost the same as dromaeosaurids.
In the same way that Rhamphorhynchoidea developed directly into Pterodactyloidea. There are no transitional fossils. One developed directly into the other."
It is a corruption of my words to imply that I am presenting the idea of "massive single-generation saltational changes." Can others here understand that?
Now that we see that saltations are eminently feasible, we can see that all that talk about physical reproductive isolation was just a dead end.
That sort of "explanation" is based on old thinking. On an old understanding of the structure and the dynamics of the genome.
With the current understanding that novelty can be created "with a limited number of genes, and a limited number of mutations [changes]" we see that all the evidence points to saltations.
The new understanding of the genome changes everything. It seems that the ramification of this new knowledge has not yet affected the rest of evolution theory thinking.
It will probably take time.
I can see why Moran would be trapped in the old way of thinking. He is near retirement.
But why the rest of you folks hold onto old disproven ideas is beyond me.
Perhaps the folks here feel they need the authorities blessing before they are allowed to actually factor in the new evidence about the genome and its processes.
No doubt that official blessing will come sometime.
But for me, it is a lot more interesting to accept the new evidence and work with it.
There are additional details in the other thread:
http://sandwalk.blogspot.com/2011/02/facilitated-variation.html
There once was a poster, Anonymous,
Who's refusal to listen was ominous,
With the traffic one way,
Only he can say,
Why he stays here and continues boring us.
An interesting group, the Anonymids,
A paraphyletic sub-group of hominids,
Their identities veiled,
Their coherence de-railed,
They still moan, "I didn't say what you think I did".
There once was a troll named Doug,
With nom de plume of Socrates,
But the reality was,
It was a boring old slug,
And full to the brim of Hypocrates.
So it looks like all that hand-wringing about the Rhett Daniels case was just for show.
People here are quite accepting of that sort of behavior.
Here is what Dr. Moran said of Rhett Daniels.
"Rhett Daniels seems to have forgotten that there are some things that are both wrong and evil."
Given what goes on on this blog, one has to wonder how Moran can make that statement.
An anonymous poster, could it be Doug Dobney,
With his copy and paste did violate thee,
Rhett Daniels, hand-wringing,
The vomit, up-bringing,
Oh Moran why do you continue to persecute me ?
I should have said "facilitated variation".
To be precise "facilitated genotypic variation".
As I argued here: "http://talkrational.org/showthread.php?p=1509036#post1509036" ichthyosaurs developed into mosasaurs which then developed into whales. There were no intermediate stages, the changes were saltational and occurred within a single generation in each case. Only misinterpretation of the fossil evidence prevents recognition of this relationship.
It is a corruption of my words to imply that I am presenting the idea of "massive single-generation saltational changes." Can others here understand that?
Hey Doug Dobney, do guests at the Moffat House know you're insane?
As the personal attacks escalate it has become quite obvious that my position is correct. Will anyone here acknowledge this?
Continuing on. Mosasaurs developed into whales. The evidence is quite convincing. Further, whales then developed into cats. Would anyone like to contribute to this line?
It is important to people to shut down any ides outside the mainstream. By any means possible.
Including the most evil means.
I wonder how Moran's students feel about this.
And I wonder how those who link to this blog feel about this.
No doubt the disturbed person who is copying my style here will have some "clever" response.
Eventually we may even have the death threats. Stated as a joke of course.
This is all so sad.
... whales then developed into cats.
Spoof.
Let those of us interested in serious discussion return to the ideas I am presenting.
We have seen that the Pagel study shows us that instances of large genetic reorganizations (saltations) generate new species, and that novelty can be created "with a limited number of genes, and a limited number of mutations."
Current dogmatic thinking is that multiple speciation events result in "radiations" of species from a single ancestral species through "cladogenesis."
This is only correct at the genus level and below. Speciation above the genus level can only occur through "anagenesis" that happens in parallel along separate lineages.*
*The parallel anagenetic speciation above the genus level is directed by the intelligence of Nature.
The link above is from the disturbed individual who has corrupted the discussion by mimicking my posts.
This means that people cannot be sure which come from me and which from the disturbed hater.
It is not enough for this ill individual to slur me and attack me and my family on the web and off the web. He goes the extra step of confusing people about what I am saying.
This all stems back, to how desperate people are, to keep any ideas outside the mainstream from even being presented.
The fact that nobody disowns this behavior means that everyone else is complicit in this vile behavior.
To attack me is bad enough but to attack my wife and family is beyond outrageous. That is what your silence is condoning.
Turning back to the topic at hand Now that we see that all the evidence
points to saltations which then developed into primitive dromaeosaurid fossils.
And I have presented my ideas to.
How closed minded you are.
blogspot.
The laws of relativity are clear on this point.
It is not simply the record of the actual events conform to and the pterosaurs
to modern birds It is believed that dinosaurs and the Galliformes are secondarily
flightless landbirds.
On an old understanding that novelty can be created with a limited number
of people and groups who are groping toward a new understanding of the structure
and the dynamics of the genome.
Now that we see that all light from a candle or from a super-sun sooner
or later fills the entire universe of space and time.
I simply build on the biological evidence.
orgwikiSpeciesDefinitionsofspecies To truly get an idea of evolutionists
who think there is no need for the intelligence of nature is undeniable.
orgshowthread.
Only misinterpretation of the fossil evidence.
Perhaps it is just a new species is for some reason a frightening idea to
evolutionists.
Can others here understanding of the structure and the dynamics of the genome
changes were saltations.
These paradoxes and oddities.
htmlcomments Advanced pterosaurs were Ornithodira -- Dinosaurs Ornithodira
-- Pterosaurs developed directly into Pterodactyloidea.
Including the purple group we see that all the evidence prevents wider acceptance
of the ideas I am presenting While people considered as the article implied.
In this respect it is closer to kinds !
On an old understand that Now that we see that all light from a candle or
from a super-sun sooner or later fills the entire universe of space and time
would appear from the various quotes articles and books that I have listed
in this blog feel about this.
orgshowthread.
There are only advanced pterosaurs developed into primitive dromaeosaurid
fossils.
It is not as easy to conceptualize and perceive levels abov
They explain how the individual organism can change from a passive target of natural selection to a central player in the -billion-year history of evolution.
There are only advanced pterosaur fossils and primitive dromaeosaurids.
It seems that the ramification of this new knowledge has not yet affected the rest of evolution theory thinking.
Only misinterpretation of the fossil evidence.
As Bernhard Haisch put it. In the reference frame of light there is no space and time.
The first level of subtle body beyond the physical which I called template is called in some systems the etheric body or etheric double etherial body
or life force and can be seen by the senses.
People have commented on the fact that I cut and paste. It is a living intelligence with consciousness.
It seems that the ramification of this new knowledge has not yet affected the rest of evolution theory thinking. Everybody knows that talk of kinds is heresy.
But this is also not worth arguing about.
Evolution theory is not capable of explaining the speciation of new types of creatures. They have too much invested in being a skeptic.
The new understanding of the structure and the dynamics of the genome. How closed minded you are. In other words it is not simply the record of the actual events but of the patterns and forms that physical events conform to and the personal manifestations of those patterns.
The outer periphery of a population's habitat tends to be extreme hence the reason range expansion is kept in check.
You do not realize how very peculiar you folks are in the total population.
The issue is that they are still the same type of creature on the one hand and the speciation of a new type of creature on the other hand.
As a general rule a different type of creature is a different genus.
As in all aspects of this subject it takes thought and analysis to see where to draw lines.
Jesus Christ on a plastic crutch!!!
You folks've been duped and duped good. This Anonymous dude must be rolling on the floor laughing till it hurts.
I mean, c'mon, have any of you actually gone and looked at that pteranodons to turkeys site?
It's an effing PARODY, like Landover Baptist Church. Took me like three seconds to figure that out.
Grow up, dudes. Sheesh!
The disturbed hater who has corrupted the discussion by mimicking my posts has slurred me and attacked me and my family.
This ill individual has done so because I am presenting ideas outside the mainstream that will ultimately supplant Darwinism and quite possibly make me the most famous scientist in history.
Here is an example of a hating death threat against me and my family I have received from this sick person.
"Hey asshole, in two hundred years you and everybody you know will be dead and not one single person will give a flying fuck about your harebrained schemes."
The disturbed man finds more ways to spew his hatred.
It is amazing that Moran tolerates this on his blog.
We must conclude that Moran condones it, given how many times I have brought it to his attention and explicitly asked him to not allow it.
This thread is probably irredeemably derailed by the Anonymouses, but I have aquestion about the original central dogma.
From the first page it says that the central dogma is that inforation can't be passed from proteins to either DNA or RNA. Since proteins are strings of amino acids, how could that even happen?
Anonymous said...
We must conclude that Moran condones it, given how many times I have brought it to his attention and explicitly asked him to not allow it.
Leave your martyr complex at home.
If someone approaches you on the street, or sends threatening letters to you home, we are behind
you.
But, people saying "that is dumb" to what you have posted is what you have to expect. Come on to a science blog with ideas of ancient earth astronauts, and "intelligent nature" and you are going to get laughed at.
Anonymous said...
"This means that people cannot be sure which come from me and which from the disturbed hater."
Ponder that for a moment. If blatant mockery of your posts is indistinguishable from your posts, what does that imply regarding the content of your posts?
I will not be mocked. It is amazing that Moran tolerates this on his blog.
We must conclude that Moran condones it, given how many times I have brought it to his attention and explicitly asked him to not allow it.
The ideas I have been presenting will revolutionize evolutionary thinking.
Those here who mock my ideas will find themselves marginalized when those ideas gain wide acceptance.
@Fred
From the first page it says that the central dogma is that inforation can't be passed from proteins to either DNA or RNA. Since proteins are strings of amino acids, how could that even happen?
I think that's why Crick felt emboldened enough to cast it as a 'dogma'. The translation table for the genetic code is held within the set of aminoacyl tRNA synthetases that tack each specific amino acid onto the end of the tRNA molecule(s) holding relevant codons for the particular aaRS.
To reverse this would entail uncoiling a protein and finding some means to translate back to a triplet (picking one where there is redundancy at one or more positions). This reverse code would need a completely different translation mechanism that would need to track evolutionary changes in the RNA -> protein system in order to preserve the mapping in both directions (which is already not one-to-one). It would also need a triphosphate-terminated version of the triplet, or a means of specifying the triplet sequence to a process of single-triphosphate-base polymerisation, since polymerisation needs that energy.
As you say, hard to see how this could work.
Anonymous posted on Monday, September 05, 2011 1:13:00 AM Toronto time.
If this is the genuine Anonymous, and if the genuine Anonymous lives in Ontario, this is an unhealthy time for posting: losing sleep. If so, Anonymous, it is healthier for you to stop hanging around on this blog.
On the other hand, the post reads so far out it might not be genuine at all.
@Fred. Yes, I think that is kind of the point. "The Central Dogma" as defined by Crick has not come close to being refuted. Purely theoretically, reverse translation could be possible but we have never even seen hints of such a thing. (NB. Even prions don't violate The Central Dogma because they do not change the sequence, only the structure.) It seems obvious sixty years on but I do not think it was so clear at the time.
On the other hand, the dumbed down (wrong) "Central Dogma" where we are concerned with the flow of any information, not just explicitly sequence information, has been refuted so long ago and so many times that it is not even worth considering as a universal rule. Hence the confusion/irritation when people claim to have refuted "The Central Dogma" - they're just attacking a pre-shredded straw man.
(As for the Anonymids - I'm just deleting anything posted by Anonymous without reading it now. Their posts have gone beyond pointless. I was about to unsubscribe altogether until I saw your post!)
@Fred (& Alan Miller). Just to clarify, when I say "Purely theoretically, reverse translation could be possible", I do mean with a completely new set of molecular machinery. I'm not implying that it is possible with the known machinery - as Alan Miller explained very nicely.
@Alan Miller and cabbagesofdoom,
Thanks for your posts. I'd been scratching my head, thinking I was missing something fundamental.
the other Jim posted:
"If someone approaches you on the street, or sends threatening letters to you home, we are behind
you."
And if someone sends threatening emails to my personal email?
Is that something you find acceptable?
Or if someone threatens to come to my house and kill me and my family?
How about that?
Or if they make threatening phone calls?
When you open the door how are you going to determine how far it goes?
Do you not get it?
And if someone sends threatening emails to my personal email?
Is that something you find acceptable?
Or if someone threatens to come to my house and kill me and my family?
How about that?
Or if they make threatening phone calls?
None of these are acceptable. See the posts on "Mabus".
Have any of these happened?
None of these are acceptable. (see The other Jim)
Have any of these happened?
Actually, I would not take the word of Anonymous if he said 'yes' to the question. Not because it might not be possible in principle, but because Anonymous has posted such impossible statements (and here I'm not referring to the bunch from this weekend) that I would doubt anything he says.
Anonymous said...
When you open the door how are you going to determine how far it goes?
This shows the items on the list before are hypothetic rather than factual.
The other Jim is right. Threats of this nature of any kind are not acceptable. If you are receiving threats, I recommend contacting the police and/or your/their ISP. I'm not sure there is much we can do here except say: No, it is not acceptable.
I haven't been reading all the Anonymous posts but has someone actually threatened you here, in these comments?
Here is a post from the other Jim referencing my earlier post:
"And if someone sends threatening emails to my personal email?
Is that something you find acceptable?
Or if someone threatens to come to my house and kill me and my family?
How about that?
Or if they make threatening phone calls?"
"None of these are acceptable. See the posts on "Mabus".
Have any of these happened?"
Notice that the Other Jim did not quote my entire post which was:
"And if someone sends threatening emails to my personal email?
Is that something you find acceptable?
Or if someone threatens to come to my house and kill me and my family?
How about that?
Or if they make threatening phone calls?
When you open the door how are you going to determine how far it goes?
Do you not get it?"
Notice the sly partial quote from the other Jim. Leaving out the significant part:
When you open the door how are you going to determine how far it goes?
Do you not get it?"
@Allan Miler would need to track evolutionary changes in the RNA -> protein system in order to preserve the mapping in both direction
How much has the transcription and translation system changed since say the origin of eukaryotic cells ?
My (admittedly cursory) investigation indicates that this process would be highly conserved.
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