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Author Topic:   Flow Chart from DNA to Amino Acid
NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 1 of 23 (484028)
09-25-2008 7:47 PM


Hello,
I just want to post a flow chart that I did based on my limited research from DNA to Protein to possibility of life. My questions are:
1) How can I post the flow-chart if I'm allowed?
2) Would members be kind enough to make corrections thereto?
3) Can I accompany the flow chart with just 6 or so questions without me replying. ( I just want to know what's on the mind of some members).

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RAZD
Member
Posts: 20156
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


Message 2 of 23 (484040)
09-25-2008 9:11 PM
Reply to: Message 1 by NOT JULIUS
09-25-2008 7:47 PM


Welcome to the fray Doubting Too

1) How can I post the flow-chart if I'm allowed?

(1) make it a picture (jpg etc)
(2) post picture to a photo sharing website
(3) find the url for the picture
(4) post [img]http://www.anthroposophie.net/bilder/Einstein2.gif[/img] and it becomes

To control image size using the thumbnail function use

[thumb=500]http://img170.imageshack.us/img170/3677/chromosomesonetofivefo3.jpg[/thumb]

and it becomes:


Click to enlarge

You can still access the full size picture by clicking on it, thus information is not lost in the reduction to fit the pages here.

You can use almost any number to set the width, the default is 80, but the maximum should not be more than 500 to fit most screens. The image is also automatically centered (cool feature Percy!).

Note: using this to make small pictures larger will result in "pixilated" blurring.

2) Would members be kind enough to make corrections thereto?
3) Can I accompany the flow chart with just 6 or so questions without me replying.

Sure.

Enjoy



ps - as you are new here, some posting tips:

type [qs]quotes are easy[/qs] and it becomes:

quotes are easy

or type [quote]quotes are easy[/quote] and it becomes:

quote:
quotes are easy

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This message is a reply to:
 Message 1 by NOT JULIUS, posted 09-25-2008 7:47 PM NOT JULIUS has responded

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NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 3 of 23 (484125)
09-26-2008 4:12 PM
Reply to: Message 2 by RAZD
09-25-2008 9:11 PM


flow chart
Here's is the two-page flow chart. Thanks, Razd & Asqara.

Click to enlarge


Click to enlarge

Edited by Doubting Too, : not working

Edited by Doubting Too, : No reason given.

Edited by Doubting Too, : No reason given.

Edited by Doubting Too, : No reason given.


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 Message 4 by Asgara, posted 09-26-2008 4:23 PM NOT JULIUS has responded

    
Asgara
Member (Idle past 593 days)
Posts: 1783
From: Wisconsin, USA
Joined: 05-10-2003


Message 4 of 23 (484127)
09-26-2008 4:23 PM
Reply to: Message 3 by NOT JULIUS
09-26-2008 4:12 PM


Re: flow chart
you need to end each thumb tag

I'm not linking real photos but you can hit the "peek" button at the bottom right of this message and see how it's done.


Click to enlarge




Click to enlarge

I've never used flicker for this, but Photobucket works. It's specifically for putting images live to be used on the net.

Edited by Asgara, : No reason given.


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NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 5 of 23 (484131)
09-26-2008 4:47 PM
Reply to: Message 4 by Asgara
09-26-2008 4:23 PM


Re: flow chart
Hi A,
Please check if it works now.

DT


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Dr Jack
Member (Idle past 396 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 6 of 23 (484132)
09-26-2008 4:50 PM
Reply to: Message 5 by NOT JULIUS
09-26-2008 4:47 PM


Re: flow chart

This message is a reply to:
 Message 5 by NOT JULIUS, posted 09-26-2008 4:47 PM NOT JULIUS has responded

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NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 7 of 23 (484135)
09-26-2008 4:55 PM
Reply to: Message 6 by Dr Jack
09-26-2008 4:50 PM


Re: flow chart
Hi Mr J,
I think I've followed your format--based on peek. Like this?


Click to enlarge


Click to enlarge

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Hyroglyphx
Member
Posts: 5829
From: Austin, TX
Joined: 05-03-2006
Member Rating: 2.0


Message 8 of 23 (484139)
09-26-2008 5:58 PM
Reply to: Message 7 by NOT JULIUS
09-26-2008 4:55 PM


Re: flow chart
Like this?

Looks good to me. You're all set, buddy.


“Tu ne cede malis sed contra audentior ito"

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NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 9 of 23 (484142)
09-26-2008 6:00 PM
Reply to: Message 7 by NOT JULIUS
09-26-2008 4:55 PM


Re: flow chart from DNA to Protein to Life
I hope you are able to access the flow chart ( #3 message). And, I hope that my flow chart explains the basic transformation from DNA to protein to life. If not, please correct.

My related questions both to IDs and believers in evolution are:

1. DNA is called the book of life. Can anyone make a book--that makes sense--by just throwing letters randomly?

2. Genetic codes and information are embedded in DNA. Is not intelligence required to decode and process information?

3. The cell has a "complex copying" machine that replicates DNA's to RNAs. Which is more reasonable to believe that intelligence was needed to make that copying machine, or was it random chance that did it?

4. The actual process from DNA to protein to life is a million times more complicated than this flowchart. As this flow chart required intelligence (though limited) to make, so should the more complex process require intelligence. Agree / Disagree? Please give reason.

5. What did Miller's failed experiment in 1953 prove?
a) that it requires blind chance to produce "left handed" amino acids--the building block of life? Or, did it prove that the chance of life coming to existence by mere chance is mathematically impossible?

6. Darwinian evolution--as taught in school--says that all living things came to existence because of unguided natural processes. On the other hand, intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not by undirected processes such as natural selection. Considering the above flowchart--which hopefully simplified the picture--which is more reasonable to believe?

Edited by Doubting Too, : clarity


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kuresu
Member (Idle past 804 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 10 of 23 (484146)
09-26-2008 7:02 PM
Reply to: Message 9 by NOT JULIUS
09-26-2008 6:00 PM


Re: flow chart from DNA to Protein to Life
Well, I think we have a sorta Gish Gallop. It's pretty clear which side you agree with (cdesignpropenentist). Each question you have is a separate topic and the answers can be found not only here, but at other sites on the internet.

DNA is called the book of life. Can anyone make a book--that makes sense--by just throwing letters randomly?

Well, I suppose there is the slightest, however remote chance, that such an outcome can happen. However, that's certaintly not the process that the ToE describes. No matter what the creos say, because everytime they bring this up they fail to show any basic understanding of what the ToE actually describes.

Genetic codes and information are embedded in DNA. Is not intelligence required to decode and process information?

Are we talking Dumbski's information theory here? It's a junk information theory. If we want to play loose with information definitions, consider this. All life responds to stimuli (not necessarily all stimuli, but at least one). In this sense, all life decodes and processes information. Since life includes bacteria, and bacteria are by no means intelligent (in a classical sense), intelligence is certaintly not necessary to decode and process information.

The cell has a "complex copying" machine that replicates DNA's to RNAs. Which is more reasonable to believe that intelligence was needed to make that copying machine, or was it random chance that did it?

This would probably fall under abiogenesis, not the ToE. Further, abiogenesis certaintly does not posit "random chance" as the perpetrator. Also, the ToE does not posit "random chance" either. You're forgetting key parts of the theory and the hypotheses, thus misleading. As a side note--how can you determine whether intelligence was behind something? No one ID/creo has been able to suggest how we can succesfully determine an intelligent agent that is distinguishable from known natural causes. Overall, a bad question.

The actual process from DNA to protein to life is a million times more complicated than this flowchart. As this flow chart required intelligence (though limited) to make, so should the more complex process require intelligence. Agree / Disagree? Please give reason.

The flow chart did not require intelligence. It required knowledge. Knowledge does not equal intelligence. Complexity does not equal intelligence. Tell me, where is the intelligence in a mandelbrot set? Nature is perfectly capable of creating something more complex without any discernible intelligent agent. Which brings up the question again--how do you determine a distinguishable intelligent agent?

What did Miller's failed experiment in 1953 prove?
a) that it requires blind chance to produce "left handed" amino acids--the building block of life? Or, did it prove that the chance of life coming to existence by mere chance is mathematically impossible?

This is the question that at last gives you away. Miller's experiment was by no means a failure. It did precisely what it attempted--the creation of amino acids in a possible early-atmosphere environment. It did not attempt, nor prove* what you are claiming in "a" and "b". When you've read up on the Miller-Urey experiment, and the research and hypotheses that have been formulated since, come back to us with a better-formulated, and more accurate, question. The other two questions contained within are pointless after realizing you got Miller-Urey wrong.

Darwinian evolution--as taught in school--says that all living things came to existence because of unguided natural processes. On the other hand, intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not by undirected processes such as natural selection. Considering the above flowchart--which hopefully simplified the picture--which is more reasonable to believe?

More nonsense, I'm afraid. I was certaintly not taught that the ToE says that all living things came into existence by unguided natural processes. What precisely is an "unguided natural process" here? Further, ID/creo is a complete failure when it comes to explaining the world. Again, you have to come up with a way to determine how to succesfully distinguish an intelligent agent as the cause behind what we see--ID/creo, for all its talk, hasn't done this (or rather, all rather silly attempts have failed). ID/creo works by suggesting, "hey, you see this tiny problem here? ID can explain it, ToE can't", but ID cannot explain 99% of what we see. Further, every "problem" ID/creo has come up with is actually explainable by the ToE.

Yeah, I'm thinking Gish Gallop. And every answer I've given will either be ignored or "nu-uh!"ed. Nothing more than what the ID/creo crowd is really capable of.


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Wounded King
Member (Idle past 2386 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 11 of 23 (484149)
09-26-2008 7:14 PM
Reply to: Message 9 by NOT JULIUS
09-26-2008 6:00 PM


Re: flow chart from DNA to Protein to Life
1. DNA is called the book of life. Can anyone make a book--that makes sense--by just throwing letters randomly?

And eyes are called the windows of the soul, but I don't put windolene on them. Why is it those critical of evolution are so often incapable of understanding metaphorical language. Plus the 'throwing letters randomly' strawman is so patently wrong it hardly seems worth pointing out that random mutation is not the sole mechanism of neo-darwinian evolution.

2. Genetic codes and information are embedded in DNA. Is not intelligence required to decode and process information?

No, if it is then where do you think the intelligence resides in the machinery of protein translation? I'd also contend that the genetic code is not embedded in DNA in any meaningful way.

3. The cell has a "complex copying" machine that replicates DNA's to RNAs. Which is more reasonable to believe that intelligence was needed to make that copying machine, or was it random chance that did it?

Another random chance strawman. It is also worth noting that DNA to RNA is not usually consider replication or copying since mRNA is significantly distinct to DNA. Also your note on DNA/RNA is pretty much pure fantasy, or do you have some references to research showing that DNA an be exported and translated to amino acids and that in such cases mRNA can be reverse transcribed and reincorporated into the genome.

4. The actual process from DNA to protein to life is a million times more complicated than this flowchart. As this flow chart required intelligence (though limited) to make, so should the more complex process require intelligence. Agree / Disagree? Please give reason.

Totally disagree. The two things are apples and oranges. Plus I think you will find the universe has both more resources and more time on its hands than you do.

5. What did Miller's failed experiment in 1953 prove?

Seriously? Did you go to 'creationisttrolls'R'us' to pick up your arguments? It proved neither of those things,nor was it a failed experiment. Could you describe what you think the experiment was intended to prove? I suspect this is yet another strawman much like your 'mere chance' comment.

6. Darwinian evolution--as taught in school--says that all living things came to existence because of unguided natural processes. On the other hand, intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not by undirected processes such as natural selection. Considering the above flowchart--which hopefully simplified the picture--which is more reasonable to believe?

Definitely the evolutionary one since it at least explains something and has some evidence to support it.

Given how bad it is your thread might be better to focus more intensively on editing your flow chart instead of all these regurgitated creationist arguments.

TTFN,

WK


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NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 12 of 23 (484151)
09-26-2008 7:23 PM


Replies to Flow chart on DNA to protein?
Thanks, Kureso and Wounded king. I am waiting for other answers specially from those who believe in ID.

Edited by Doubting Too, : No reason given.


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NosyNed
Member
Posts: 8863
From: Canada
Joined: 04-04-2003
Member Rating: 5.3


Message 13 of 23 (484154)
09-26-2008 7:26 PM
Reply to: Message 9 by NOT JULIUS
09-26-2008 6:00 PM


Random Sense
1. DNA is called the book of life. Can anyone make a book--that makes sense--by just throwing letters randomly?

Yes. If you accept misspellings and having the book come out in lots of different languages. And then if you throw away all the books that you don't like.

The DNA base-pairs are often likened to letters in an alphabet. What you forget is that almost any combination of them makes up some sort of "word" . Therefore many more random combinations make "sense" in some way. You can change some part of any string of DNA and in most cases it makes "sense". It just might not produce a very viable organism but that isn't such a concern of nature as it might be to a book publisher.

In addition, after throwing letters together you then throw away all the books that you don't like for whatever reason. This isn't going to make for a very profitable book publisher but it is the way life works. For example, about half (maybe more ) of all human "books" are thrown away before the ink is even dry. Some other percentage is thrown out before the "book" is finished "printing". This may seem very wasteful but that is the way things are done in nature and it happens to work very well. And humans are an animal that uses a low quantity, high quality approach to reproduction. Some animals operate with a throw away percentage way, way higher thant 50%.

2. Genetic codes and information are embedded in DNA. Is not intelligence required to decode and process information?

No, just chemistry. DNA is a chemical and is involved in chemical reactions which produce proteins.

3. The cell has a "complex copying" machine that replicates DNA's to RNAs. Which is more reasonable to believe that intelligence was needed to make that copying machine, or was it random chance that did it?

Since we know that some simple copying machines can arise through chemistry it isn't too unreasonable to surmise that more complex machines might too. But we don't know. To assume an intelligence because we don't know would have us still thinking that lightening is tossed at us from the hand of Zeus.

4. The actual process from DNA to protein to life is a million times more complicated than this flowchart. As this flow chart required intelligence (though limited) to make, so should the more complex process require intelligence. Agree / Disagree? Please give reason.

Disagree. We know that very, very complex things can arise without intelligence.

5. What did Miller's failed experiment in 1953 prove?
a) that it requires blind chance to produce "left handed" amino acids--the building block of life? Or, did it prove that the chance of life coming to existence by mere chance is mathematically impossible?

Miller's experiment has been outdated for decades so why does it matter what it proved? At the time it was a big deal because it wasn't clear that any basic building blocks of life could arise in such a fashion (I guess because they were considered to be "too complicated". This was proved to be wrong.)

6. Darwinian evolution--as taught in school--says that all living things came to existence because of unguided natural processes. On the other hand, intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not by undirected processes such as natural selection. Considering the above flowchart--which hopefully simplified the picture--which is more reasonable to believe?

Since we can use evolutionary processes to produce complicated (very) outcomes and the nature of these outcomes have characteristics that living things also have the most reasonable thing to accept is that living things were, indeed, produced by similar processes. This is especially true when we can see the process going on before our very eyes. To think that there is any direction involved would be silly since we can see it happening without any evidence whatsoever for direction.


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RAZD
Member
Posts: 20156
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


Message 14 of 23 (484156)
09-26-2008 7:30 PM
Reply to: Message 9 by NOT JULIUS
09-26-2008 6:00 PM


questions and PRATTs
Hello Doubting Too

I hope you are able to access the flow chart ( 3/7 message). And, I hope that my flow chart explains the basic transformation from DNA to protein to life. If not, please correct.

It seems to cover the basics of how proteins are made in modern evolved cells with highly advanced DNA (3 billion years in the making).

1. DNA is called the book of life. Can anyone make a book--that makes sense--by just throwing letters randomly?

I can call the tree in my back yard the book of life, but that doesn't mean that it's true - that I can open up the pages and see all there is to know about biological life.

Now you can open a book randomly and read each page and what you end up with is a random jumbling of ideas.

Or you can select to open pages in sequence, and when you do that you end up finding less jumbling and much more ordering of ideas.

Just as selection is the key to reading the book, selection is the key to making the book: the words and Ideas are selected to be in a particular place.

The question is how the selection occurs.

2. Genetic codes and information are embedded in DNA. Is not intelligence required to decode and process information?

No, the DNA is the genetic "code" and all it has is four letters arranged in various orders.

For us to understand the process we do need to apply a little intelligence and a lot of study, but that doesn't mean that intelligence is needed to make it.

3. The cell has a "complex copying" machine that replicates DNA's to RNAs. Which is more reasonable to believe that intelligence was needed to make that copying machine, or was it random chance that did it?

The "complex copying" machine is just molecules bonding according to the basic rules of chemistry, which means that some things can happen and others can't.

Just because something seems reasonable to you doesn't mean it is true: nature is indifferent and completely unaffected by opinion - yours, mine, anyone's.

4. The actual process from DNA to protein to life is a million times more complicated than this flowchart. As this flow chart required intelligence (though limited) to make, so should the more complex process require intelligence. Agree / Disagree? Please give reason.

Argument from incredulity is another logical fallacy that does not mean your conclusion is valid, and you are also committing the

all {A} is {B}
{B} exists
therefore {A} exists

fallacy.

Obviously not all {B} is necessarily {A} so you need to demonstrate there is no {B} that is not {A} before you can make this conclusion.

A snow flake is design but is not designed. The pattern in a kaleidoscope is pretty, but the reality is that it is a jumble of colored bits seen through mirrors: the point of view may see a pattern that does not in fact exist.

5. What did Miller's failed experiment in 1953 prove?

Who said it failed? Not Urey nor Miller

http://en.wikipedia.org/wiki/Miller-Urey_experiment

quote:
The Miller-Urey experiment (or Urey-Miller experiment) was an experiment that simulated hypothetical conditions present on the early Earth and tested for the occurrence of chemical evolution. Specifically, the experiment tested Oparin and Haldane's hypothesis that conditions on the primitive Earth favored chemical reactions that synthesized organic compounds from inorganic precursors. Considered to be the classic experiment on the origin of life, it was conducted in 1953 by Stanley L. Miller and Harold C. Urey at the University of Chicago.[1][2][3]

Organic compounds were formed, therefore it was a success.

a) that it requires blind chance to produce "left handed" amino acids--the building block of life?

But that was not the goal of the experiment. All they needed to do was produce amino acids. They did.

We also know that the early earth was bombarded by amino acids that formed in space and were carried to the earth by meteors. We have recovered some of these amino acids from meteors that have landed on earth in recent years.

For more information see Building Blocks of Life and note that this is nearly 3 years out of date, and abiogenesis is a rapidly growing and evolving field.

We know the building blocks were available on the early earth. The question is how the selection occurs.

Or, did it prove that the chance of life coming to existence by mere chance is mathematically impossible?

Curiously nothing about reality can be proven nor disproven by math. Math can only model reality, not control it: if the model does not predict what actually occurred then the model is wrong.

See the old improbable probability problem for a discussion of the problems with mathematical calculations and what valid conclusions can be reached from mathematical models.

6. Darwinian evolution--as taught in school--says that all living things came to existence because of unguided natural processes.

That may be what you were taught in your school, however it is not either "Darwinian evolution" (pre-genetics) nor is it Biological evolution (post-genetics).

Nor is it true.

Here is a Primer on Biological Evolution from Berkely (where they teach university level evolution). Consider this a remedial evolution course to bring you up to speed on what evolution is really all about.

quote:
The Definition:
Biological evolution, simply put, is descent with modification. This definition encompasses small-scale evolution (changes in gene frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations). Evolution helps us to understand the history of life.

I hope you read the whole thing, as there is a lot of valid and valuable information there. You would probably do best if you forgot everything anyone said to you about evolution first, no matter what the source was.

If you don't read the whole thing, you should at least check out the section on Natural Selection

quote:
Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift.

Darwin’s grand idea of evolution by natural selection is relatively simple but often misunderstood. To find out how it works, imagine a population of beetles:
...
4. End result:
The more advantageous trait, brown coloration, which allows the beetle to have more offspring, becomes more common in the population. If this process continues, eventually, all individuals in the population will be brown.

If you have variation, differential reproduction, and heredity, you will have evolution by natural selection as an outcome. It is as simple as that.


Natural selection is not an "unguided natural processes" as it is a process that discriminates against those with less advantageous traits in favor of those with more advantageous trait.

Remember that the question is how the selection occurs.

On the other hand, intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not by undirected processes such as natural selection.

So the continuous evolution of bacteria that cause any number of lethal diseases, the change in them every year that allows them to survive the latest antibiotics developed by intelligent beings, the fact that last years flu vaccine is no good this year is "best explained by an intelligent cause" ??? My conclusion from this is that this "intelligent cause" favors bacteria over humans: it keeps trying to kill us off and let them live.

Considering the above flowchart--which hopefully simplified the picture--which is more reasonable to believe?

Again, what is "reasonable to believe" has no bearing on what actually happens in the world of reality. Reality is, sadly, completely unaffected by belief, no matter what that belief involves.

If you really want to study the problem from a scientific point of view, rather than take anyone's word for it, I would suggest starting from the bottom up:

(a) what do we know existed on an early earth? amino acids. (see what you can find about what amino acids were common on the ancient earth).
(b) what do we need as a minimum to start evolutionary processes? replication with variation and selection. (see what you can find out about 'LUCA' and replicating molecules).

Take it from there.

Enjoy.

Edited by RAZD, : open book


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

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 Message 9 by NOT JULIUS, posted 09-26-2008 6:00 PM NOT JULIUS has responded

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NOT JULIUS
Member (Idle past 2766 days)
Posts: 219
From: Rome
Joined: 11-29-2006


Message 15 of 23 (484159)
09-26-2008 7:32 PM
Reply to: Message 10 by kuresu
09-26-2008 7:02 PM


Re: flow chart from DNA to Protein to Life
Kuresu,
Please explain to me the following. I'm not familiar with them.I'm just a kid, you know.
a) ToE
b)Dumbski's information theory.

thanks,
DT


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