Annoying creationists

[articulett]

I think the right sorts of chemicals would start evolving all on their own. How gene precursors became genes I have no idea.

~~ Paul

His theory has something to do with data coming from the sun an oscillations...but it presumes a "starting point" for replication...and evolution doesn't really have neat categories or agreed upon starting points...that goes for replication as well.

Prions are more like "things" than life forms (as are viruses), but they have life-ish properties:

Cause of Alzheimer's located? Sep 22, 2006
Its similar to how one crystal can spark others to form, a domino effect very similar to that seen in mad cow disease and other neurodegenerative diseases that are caused by abnormally shaped proteins called prions. Click for related content. (MSNBC -- Health)


John seems to think that something other than natural forces need to supply the impetus to replicate...but replication is a continuum...and there are fuzzy lines as to what is and isn't a replicator (a semantic game John likes to play which is interesting considering that he thinks "hypothesis" and "theory" are scientific semantic games that he refuses play). John says he agrees with Behe that cells are the items that should count as replicators--not DNA/RNA. But I have no idea how he squeezes his oscillation/data stream hypothesis into that framework...but my contention is, that no-one else understands what he is saying either.

 

[kleinman]

Annoying Creationists

...I must have missed that explanation of the selection pressure that would lead to the evolution of a gene de novo, do you mind repeating it?

Right! Just ignore the world, k. Ignore the whole rest of my post. Ignore everything in the thread. Ignore the attempts to teach you a little about genetics which you have made no attempts to even grasp let alone master.

Skeptigirl, I know you are having a hard time coming to grips with this but there is no selection process that would lead to the evolution of a gene de novo. Without this selection process, you have no macroevolution. Mutation and natural selection can not and does not do what is hypothesized in the theory of evolution. You have succumbed to peer pressure on this issue not the truth.

 

[Skeptic Ginger]

-

They would be my peers. Unlike you who has only ideas of grandeur in your corner. And of course you continue to ignore the whole rest of my post.

 

[Yahzi]

Knighted for his services, acknowledged as the father of modern NZ university methods, he was hardly an idiot. Sure, some of his own work is now falsified, but being wrong doesn't make him an idiot. He led UK philosophy for nearly half a century.

What have you done?

I'm sorry, but to participate in this discussion, it is necessary that you provide something other than logical fallacies.

 

[Yahzi]

In my opinion, Popper was the best philosopher of the 20th century but you are free to differ.

Aside from being wrong... why, yes.

Thank you for telling me, again, that you have not read my work

Astonishing! He can be taught!

I now understand that you have not read my work and that you know nothing about the ideas which led me to it.

Is it too much to ask that you describe your work in an executive summary before requiring us to read every turgid syllable you cranked out?

Perhaps that is why I find your comments trite?

From where I'm sitting, you don't appear to find my comments trite. You appear to find my commments unanswerable.

Which is why you go to such great lengths to not answer them.

 

[Yahzi]

Really? Why?

Have you read the book in question?

No?

Are you, perhaps, expecting us to explain it to you before you read it? Perhaps in an executive summary?

 

[The Atheist]

I'm sorry, but to participate in this discussion, it is necessary that you provide something other than logical fallacies.

Which is science-speak for answering the question in the negative.



(p.s. Read a couple of your own posts, first.)

 

[John Hewitt]

From the little I've read at Wikipedia, prion replication is still a somewhat mysterious process, which some scientists suggest violates the "central dogma of molecular biology."

So, the point is, and it seems to back your own point, that some molecular structures may be capable of reproducing even though they are not based on RNA/DNA.

If so, then the prion falsifies Kleinman's hypothesis that you need a gene to get RMNS started.

As I say, if I've got that mechanism right, the actual replication of prions is from the genome but the "infectivity" comes about because of its autocatalytic change. The autocatalytic change is not a replicator in itself.

Eigen got his Nobel for the hypercycle approach to replicators, a hypercycle being essentially a chemical oscillator that is subject to evolution. These are related to autocatalysis because one may describe a chemical oscillator as two linked autocatalytic reactions, the product of each inhibiting the formation of the other. That pattern of feedbacks is one way of getting an oscillation but it cannot happen by chance. Self-sustaining chemical oscillation requires a very specific mixture of chemicals, a regular free energy supply and a boundary to keep the chemicals together.

My work notes that there is another source of oscillations - driven oscillations due to the sun's daily cycle. I argue that, although these driven oscillations are not self-replicating, they are subject to selection and that their selection eventually leads to a truly self-replicating protocell.

 

[Ivor the Engineer]

I've just been reading a bit more of John’s argument about why explaining evolution using genes is flawed. My main questions for John or anybody else here are:

Is anyone seriously claiming genes and evolution are inextricably linked?

Isn’t the word ‘gene’ shorthand for something like ‘molecular data storage device’, along with other things? Don’t scientists implicitly know this?

Isn’t trying to explain humor or other social behavior using genes like using the state of transistors in a processor to understand the operation of Windows?

Perhaps I’ve misunderstood what scientists are attempting to do in genetics, but I thought it was explaining human evolution at a physiological level, with some physiology having direct impact on behavior.

Psychology is the study of human behavior. Maybe one day it will coalesce with genetics (I doubt it), but at this stage they are distinct areas of study, except for the impact physiology has on behavior.

As I understand it (now probably showing my ignorance), all you need to have a system that can evolve is:

An energy source
A memory store
External stressors that can affect a particular memory stores’ survival chances
Reproduction of memory store with modification/error

As for what happened at the very beginning of life, I’m not that concerned. The answer has no application today. All ideas about it will be little more than hypotheses since I doubt anyone has the patience (or environment) required to do the experiments that would take billions of years to complete to provide supporting evidence.

 

[Dr Adequate]

Skeptigirl, I know you are having a hard time coming to grips with this but there is no selection process that would lead to the evolution of a gene de novo. Without this selection process, you have no macroevolution. Mutation and natural selection can not and does not do what is hypothesized in the theory of evolution. You have succumbed to peer pressure on this issue not the truth.

You know I said you should find out what "selection" means?

You should also add the word "truth" to the list of words you should look up. It's a fascinating concept, though you might not enjoy it as much as the rest of us.

 

[Indolent Wretch]

Design's definition implies an intent.

Indeed, the waves do not design the shore.

 

[John Hewitt]

I've just been reading a bit more of John’s argument about why explaining evolution using genes is flawed. My main questions for John or anybody else here are:

A. Is anyone seriously claiming genes and evolution are inextricably linked?

B. Isn’t the word ‘gene’ shorthand for something like ‘molecular data storage device’, along with other things? Don’t scientists implicitly know this?

C. Isn’t trying to explain humor or other social behavior using genes like using the state of transistors in a processor to understand the operation of Windows?

D. Perhaps I’ve misunderstood what scientists are attempting to do in genetics, but I thought it was explaining human evolution at a physiological level, with some physiology having direct impact on behavior.

E. Psychology is the study of human behavior. Maybe one day it will coalesce with genetics (I doubt it), but at this stage they are distinct areas of study, except for the impact physiology has on behavior.

F. As I understand it (now probably showing my ignorance), all you need to have a system that can evolve is:

An energy source
A memory store
External stressors that can affect a particular memory stores’ survival chances
Reproduction of memory store with modification/error

G. As for what happened at the very beginning of life, I’m not that concerned. The answer has no application today. All ideas about it will be little more than hypotheses since I doubt anyone has the patience (or environment) required to do the experiments that would take billions of years to complete to provide supporting evidence.

Some interesting points, though still rather pejorative.
A. How about Dawkins and his followers, which means the great majority of biologists? Dawkins is quite explicit genes began as and are replicators. I disagree.

B. No, but they need to.

C. I do not understand this point.

D. In many human behaviours, social and genetic data intermingle, humour being an example. Things like laughter and crying are, in part, genetically programmed responses to social situations.

E. See above.

F. I am glad you are moving toward a systems view of evolution, I agree with it. The system needs the properties of a Von Neumann machine plus variation and selection. One of the more influential advocates of the systems view was Gregory Bateson, who's father had brought the gene approach to the fore.

G. You are entitled to your opinion but a great many people are concerned with what happened at the beginning of life. I think that, unless sensible answers are developed, there will always be a big black box at the centre of evolutionary theory.

 

[Yahzi]

Which is science-speak for answering the question in the negative.

What is "science-speak?"

Your entire post was an argument from authority. You did not provide logical reasons for Popper's correctness; you provided authorative ones. Are you unaware that scientific truth is derived from epirical observation, not from academic honors?

(p.s. Read a couple of your own posts, first.)

I have explained why I thought your post was a logical fallacy. Perhaps you could do the same in return.

 

[Yahzi]

Eigen got his Nobel for the hypercycle approach to replicators

Your envy is showing.

My work notes that there is another source of oscillations - driven oscillations due to the sun's daily cycle.

Am I the only one who sees the parellels to this?

 

[delphi_ote]

Isn’t trying to explain humor or other social behavior using genes like using the state of transistors in a processor to understand the operation of Windows?

But you have to understand the underlying benefit of humor to a species. It developed in an evolutionary context. It may have cultural benefits, but cultural benefits tie ultimately at some level to evolutionary causes.

As for what happened at the very beginning of life, I’m not that concerned. The answer has no application today.

The origin of life will tell us a lot about just what it means to be alive and whether we should expect to find life elsewhere in the universe. We should be concerned and excited about answering this question!

All ideas about it will be little more than hypotheses since I doubt anyone has the patience (or environment) required to do the experiments that would take billions of years to complete to provide supporting evidence.

You don't have to directly observe the exact process in order to make a scientific conclusion. We'd have to toss out all of cosmology, evolution, modern geology, etc. if that was the case. You can use indirect evidence to support a hypothesis.

 

[kjkent1]

As I say, if I've got that mechanism right, the actual replication of prions is from the genome but the "infectivity" comes about because of its autocatalytic change. The autocatalytic change is not a replicator in itself.

Eigen got his Nobel for the hypercycle approach to replicators, a hypercycle being essentially a chemical oscillator that is subject to evolution. These are related to autocatalysis because one may describe a chemical oscillator as two linked autocatalytic reactions, the product of each inhibiting the formation of the other. That pattern of feedbacks is one way of getting an oscillation but it cannot happen by chance. Self-sustaining chemical oscillation requires a very specific mixture of chemicals, a regular free energy supply and a boundary to keep the chemicals together.

My work notes that there is another source of oscillations - driven oscillations due to the sun's daily cycle. I argue that, although these driven oscillations are not self-replicating, they are subject to selection and that their selection eventually leads to a truly self-replicating protocell.

I found the following link which describes prions pretty well for free info: http://www.kcom.edu/faculty/chamberlain/Website/Lects/PRIONS.HTM

Maybe you could translate the following quote into plain English for me:

In normal cells only the PrP 33-35 protein is synthesized. It is found in the neural cell membrane where it's function is to sequester Cu++ ions. In abnormal ("infected") cells, the PrP 27-30 is produced from the PrP 33-35 protein. The PrP 27-30 triggers a series of reactions that produce more PrP 27-30 proteins, i.e., PrP 27-30 induces its own synthesis. In addition to the post translational modifications, the PrP 27-30 protein differs from the PrP 33-35 protein in a single amino acid residue. Residue 178 in the PrP 27-30 contains an asparagine residue whereas the PrP 33-35 protein has an aspartate residue at this position. This causes a conformational change in the PrP 27-30 protein from an a-helix to a b-sheet. This conformational change in the PrP 27-30 protein has three effects:

• [FONT=Arial,Helvetica][SIZE=-1]1. It imparts to the PrP 27-30 protein the ability to induce the same a-helix to b-sheet conformation in the PrP 33-35[/SIZE][/FONT]
  [FONT=Arial,Helvetica][SIZE=-1] protein. This is a permanent conformational change. It thus induces its own "replication."[/SIZE][/FONT]
  [FONT=Arial,Helvetica][SIZE=-1]2. The b-sheet-forming peptides aggregate to form amyloid fibrils.[/SIZE][/FONT] [FONT=Arial,Helvetica][SIZE=-1]3. The amyloid fibrils kill thalamus neurons through apoptosis, a programmed series of events that leads to cell death.[/SIZE][/FONT]

Regarding the sun's oscillations driving your theory, how are these oscillations subject to selection?

 

[Ivor the Engineer]

But you have to understand the underlying benefit of humor to a species. It developed in an evolutionary context. It may have cultural benefits, but cultural benefits tie ultimately at some level to evolutionary causes.

I wasn't denying that. I was trying to point out that phenomenon should be analyzed at an appropriate level for the analysis to be useful. Undoubtedly genes influence all human behavior. E.g. how my genes relate to me chopping an onion or slicing bread is of little relevance to these behaviors.

The origin of life will tell us a lot about just what it means to be alive and whether we should expect to find life elsewhere in the universe. We should be concerned and excited about answering this question!

I'll concede that if it was possible to figure out the origin of life then it would be useful information to determine if life could exist elsewhere in the universe.

However, I'm still not excited by the idea of creatures a million light-years away, as I can't possibly examine or communicate with them. The only life of interest is that which can be reached by man, our scientific instruments or our two-way communications. So why not just go and find it?

As for what it means to be alive: not dead

You don't have to directly observe the exact process in order to make a scientific conclusion. We'd have to toss out all of cosmology, evolution, modern geology, etc. if that was the case. You can use indirect evidence to support a hypothesis.

True, but if I want to demonstrate a bunch of chemicals changing from not-alive to alive, or even non-replicating to replicating, I see no other method viable than an actual experiment with similar conditions to that on earth when life appeared here. Perhaps I was exaggerating the timescales: it would only take hundreds of thousands of years to perform.

 

[John Hewitt]

I found the following link which describes prions pretty well for free info: http://www.kcom.edu/faculty/chamberlain/Website/Lects/PRIONS.HTM

Maybe you could translate the following quote into plain English for me:

In normal cells only the PrP 33-35 protein is synthesized. It is found in the neural cell membrane where it's function is to sequester Cu++ ions. In abnormal ("infected") cells, the PrP 27-30 is produced from the PrP 33-35 protein. The PrP 27-30 triggers a series of reactions that produce more PrP 27-30 proteins, i.e., PrP 27-30 induces its own synthesis. In addition to the post translational modifications, the PrP 27-30 protein differs from the PrP 33-35 protein in a single amino acid residue. Residue 178 in the PrP 27-30 contains an asparagine residue whereas the PrP 33-35 protein has an aspartate residue at this position. This causes a conformational change in the PrP 27-30 protein from an a-helix to a b-sheet. This conformational change in the PrP 27-30 protein has three effects:

• [FONT=Arial,Helvetica][SIZE=-1]1. It imparts to the PrP 27-30 protein the ability to induce the same a-helix to b-sheet conformation in the PrP 33-35[/SIZE][/FONT]
  [FONT=Arial,Helvetica][SIZE=-1] protein. This is a permanent conformational change. It thus induces its own "replication."[/SIZE][/FONT]
  [FONT=Arial,Helvetica][SIZE=-1]2. The b-sheet-forming peptides aggregate to form amyloid fibrils.[/SIZE][/FONT] [FONT=Arial,Helvetica][SIZE=-1]3. The amyloid fibrils kill thalamus neurons through apoptosis, a programmed series of events that leads to cell death.[/SIZE][/FONT]

Regarding the sun's oscillations driving your theory, how are these oscillations subject to selection?

PrP 33-35 protein is likely the name of the protein product of gene PrP 33-35; the numbers are probably gel bands. Sequesters copper means it takes up copper and so prevents copper toxic effects. It state that protein PrP 33-35 can be concerted to PrP 27-30 by a reaction that is catalysed by PrP 27-30. In other words, this is an autocatalytic reaction, which they describe as "replication" but, as they realise, it is not true replication. Alpha helix and beta pleated sheet are just standard secondary conformations of proteins.
I have not seen the word amyloid before but the site defines this in terms of histology, as staining features in a light microscope - the amyloid bodies are, more a or less, a precipitate of PrP 27-30 whch kills the cell. Apoptosis is "programmed cell death" which is an important mechanism determining the developmental pathway of embryos. For example, you have separate fingers because the cells that once joined them together are programmed to die. The implication might be that this mechanism of killing is generally important in apoptosis, but I am not sure.


So far as the question on oscilations are concerned - all chemicals on the early earth were exposed to high energy events, lightning, UV etc. Some oscillations were protected from such event because of their physicochemical properties. These oscillations would have been selected. This is discussed in much more detail on my site -
http://www.sexandphilosophy.co.uk/pe04_evolution_oscillations.htm

 

[articulett]

But it's not just the sun providing the selection....nor even the energy--we have energy radioactive energy at the core of the earth. An ice crystal begets more ice crystals...this is similar to prion replication, but it isn't related to the sun. Some molecules will preferentially stick when the solution they are in washes over surfaces or evaporates. Sure, the environment selects...but your theory involves coding of information in data streams from the sun... and that's where things get fuzzy...and abiogenesis is a long way from both sex, humor, and philosophy--not to mention "free will" which you contend is a special feature of humans.

John, clarity would help. And sending people off to plow through your very unclear website without a brief summation of what it is they are supposed to be looking for or what your hypothesis is, is unfair. At least tell people what to look for. Don't you see all the people telling you that you are unclear? Has a single person been able to sum up your hypothesis? Contrast that to the article I posted.

 

[articulett]

What is "science-speak?"

Your entire post was an argument from authority. You did not provide logical reasons for Popper's correctness; you provided authorative ones. Are you unaware that scientific truth is derived from epirical observation, not from academic honors?


I have explained why I thought your post was a logical fallacy. Perhaps you could do the same in return.

Nope--he's the social buffoon whose too clueless to know that he's the buffoon he accuses everyone else of being. Why would he claim to understand logical fallacies and even claim you had made one when he seems to have not the slightest understanding of what they are? And by "science speak", I'm presuming he means basic logic. Moreover, is argument that "Karl Popper was a genius and what have you done?" was particularly inane. Instead of asking for clarification of your position--he showed his great allegiance to Popper and presumed someone would would need to have "done something" that he felt was "as worthy" to have an opinion about the worth of Popper."

Enjoy the irony of the logically fallacious asserting how logical they are and how illogical you are. And, for what it's worth, he seems to have these communication problems with many.