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Author Topic:   Design Framework for Evolution
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 1 of 81 (698215)
05-04-2013 5:13 AM


For the last couple of years I try to apply design patterns mainly from software engineering to unravel evolution. This approach resulted in different scenario's for the origin of life and the first cells, based on design paradigms. I now created a website where I present a general design framework for evolution and where I explain how life originated, how the first genome and the first cell evolved and how the design patters can be used to explain evolution in general.
-Life can be modelled on design patterns that are conceptually similar to iterative software development and using similar deisgn patterns such as encapsulation and object-orientation.
-Life evolved inside-out, meaning that we life originated by adding funcitonal layers on top of existing ones. For the eukaryotic cell this means first replicating DNA, then a nucleolus, then a nuclear lamina and the nuclear membrane before the evolution of the plasma membrane
-Ontogeny reflects the phylogeny. By looking at the dependencies between the different components of the cell and the way they are assembled during development, one can deduct the evolutionary steps. Thus, we can reverse engineer evolution and avoid irreducibly complex systems.
The website is design4evolution.net. Would like to hear your opinions on the design approach, the molecular steps I propose and the general philosophical aspects of my approach and findings.

Replies to this message:
 Message 3 by Pressie, posted 05-06-2013 7:08 AM Albert de Roos has replied
 Message 5 by Genomicus, posted 05-06-2013 6:46 PM Albert de Roos has replied

  
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Message 2 of 81 (698217)
05-04-2013 8:35 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Design Framework for Evolution thread in the Proposed New Topics forum.

  
Pressie
Member
Posts: 2103
From: Pretoria, SA
Joined: 06-18-2010


Message 3 of 81 (698364)
05-06-2013 7:08 AM
Reply to: Message 1 by Albert de Roos
05-04-2013 5:13 AM


Other life?
This one is troubling to me:
Albert de Roos writes:
It proposes that the first entity of Life was the replicating of DNA, representing also the first life cycle
Did the Designer have replicating DNA all those years ago to be called 'Life'?
What about replicating RNA, maybe that was representing the first life cycle? They do have life cycles. A virus does it.
Maybe mad cow disease represented the first life cycle? Prions?
Maybe you should try to define what you mean with the word 'life' before we can have a meaningful discussion?
Edited by Pressie, : No reason given.

This message is a reply to:
 Message 1 by Albert de Roos, posted 05-04-2013 5:13 AM Albert de Roos has replied

Replies to this message:
 Message 4 by Albert de Roos, posted 05-06-2013 10:12 AM Pressie has replied

  
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 4 of 81 (698375)
05-06-2013 10:12 AM
Reply to: Message 3 by Pressie
05-06-2013 7:08 AM


Pressie: Maybe you should try to define what you mean with the word 'life' before we can have a meaningful discussion?
I use the word Life in a purely mechanistic way and I propose that a replicating genome can be considered the first life form. Replication of a genome is the common denominator of all life and the basis of its evolution. Basically I go back in evolution (I reverse engineer evolution) and peel away all the extras that were added in evolution until I end up with something that I consider the essence and beginning of Life. The alpha and the omega of Life so to say.
Although prions and viruses at the basis of Life are very interesting to research, my work does not imply them directly. Proteins are derived from DNA, so DNA was first. Viruses are dependent on the cell machinery, so they evolved later. One could even argue that viruses are so intricately envolved in the cell's mechanisms that they have evolved as part of the cell and were never a seperate entity.

This message is a reply to:
 Message 3 by Pressie, posted 05-06-2013 7:08 AM Pressie has replied

Replies to this message:
 Message 7 by Pressie, posted 05-07-2013 6:53 AM Albert de Roos has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 5 of 81 (698404)
05-06-2013 6:46 PM
Reply to: Message 1 by Albert de Roos
05-04-2013 5:13 AM


Hi Albert de Roos,
I've read a couple of your papers in the past on the design-by-contract methodology and how it relates to biological systems and I found them quite interesting.
I have a quick question. Your approach is based on a design framework but it does not invoke an intelligent designer, correct?

This message is a reply to:
 Message 1 by Albert de Roos, posted 05-04-2013 5:13 AM Albert de Roos has replied

Replies to this message:
 Message 6 by Albert de Roos, posted 05-07-2013 6:17 AM Genomicus has replied

  
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 6 of 81 (698448)
05-07-2013 6:17 AM
Reply to: Message 5 by Genomicus
05-06-2013 6:46 PM


Hi genomicus. Yes, that is true, it does not directly invoke an intelligent designer, but also does not preclude it. Based on my reverse engineering, I propose a mechanistic scenario of how the eukaryotic cell was put together. However, when one arrives at the driving forces for this behavior, it gets a lot more difficult. Classical terms such as natural selection and random mutation seem irrelevant or useless at a macroevolutionary scale. For now, I assume that energy input in the form of day/night and seasonal changes can explain evolution, but at the moment we miss some parts of the equation.

This message is a reply to:
 Message 5 by Genomicus, posted 05-06-2013 6:46 PM Genomicus has replied

Replies to this message:
 Message 12 by NoNukes, posted 05-09-2013 12:33 AM Albert de Roos has replied
 Message 25 by Genomicus, posted 05-10-2013 1:25 PM Albert de Roos has replied
 Message 28 by shadow71, posted 05-10-2013 7:36 PM Albert de Roos has not replied

  
Pressie
Member
Posts: 2103
From: Pretoria, SA
Joined: 06-18-2010


Message 7 of 81 (698449)
05-07-2013 6:53 AM
Reply to: Message 4 by Albert de Roos
05-06-2013 10:12 AM


And organisms called DNA viruses? Are they alive?

This message is a reply to:
 Message 4 by Albert de Roos, posted 05-06-2013 10:12 AM Albert de Roos has replied

Replies to this message:
 Message 8 by Albert de Roos, posted 05-07-2013 11:16 AM Pressie has replied

  
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 8 of 81 (698471)
05-07-2013 11:16 AM
Reply to: Message 7 by Pressie
05-07-2013 6:53 AM


Viruses have a seperate life cycle that is relatively independent from the life cycle of their hosts, but they are 100% dependent on the host itself.
The problem is that we see viruses as a seperate entity able to infect cells and take cells hostage. I see them as extension of cells, pieces of DNA that have evolved to communicate pieces with other individual organism.
On a microevolutionary scale, they may be infectious agents, but they may represent powerful evolutionary tools on a higher level. In the line of my 'design framework', viruses can maybe be seen as intelligent agents that increase evolvability

This message is a reply to:
 Message 7 by Pressie, posted 05-07-2013 6:53 AM Pressie has replied

Replies to this message:
 Message 9 by Pressie, posted 05-07-2013 11:45 PM Albert de Roos has replied

  
Pressie
Member
Posts: 2103
From: Pretoria, SA
Joined: 06-18-2010


Message 9 of 81 (698544)
05-07-2013 11:45 PM
Reply to: Message 8 by Albert de Roos
05-07-2013 11:16 AM


You still haven't answered the question. Do you see DNA viruses as "life"?

This message is a reply to:
 Message 8 by Albert de Roos, posted 05-07-2013 11:16 AM Albert de Roos has replied

Replies to this message:
 Message 10 by Albert de Roos, posted 05-08-2013 6:48 PM Pressie has replied

  
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 10 of 81 (698673)
05-08-2013 6:48 PM
Reply to: Message 9 by Pressie
05-07-2013 11:45 PM


I do not see viruses as a seperate Life entity, but part of the Life cycle of other organisms. Just as I don't see a membrane transporter or a transposon as Life, but only part of it.

This message is a reply to:
 Message 9 by Pressie, posted 05-07-2013 11:45 PM Pressie has replied

Replies to this message:
 Message 11 by Pressie, posted 05-09-2013 12:05 AM Albert de Roos has replied

  
Pressie
Member
Posts: 2103
From: Pretoria, SA
Joined: 06-18-2010


Message 11 of 81 (698702)
05-09-2013 12:05 AM
Reply to: Message 10 by Albert de Roos
05-08-2013 6:48 PM


You do not consider DNA viruses as life then.
Following that, your previous description of what you regard as "life" doesn't make sense. I'll repeat part of your post for you.
Albert de Roos writes:
I use the word Life in a purely mechanistic way and I propose that a replicating genome can be considered the first life form. Replication of a genome is the common denominator of all life and the basis of its evolution.
I propose that we have a workable definition of "Life' before this thread can start properly and before I can start learning from the specialists.
I have seen how cdesign proponentsists tend to move the goalposts on the description of the word "Life" when it suits them....to such an extent that the word "Life" becomes meaningless (I think that they do it to ensure that their favourite designers can be classified as Life, even though they are supposed to be spooks).
Edited by Pressie, : Spelling and last paragraph

This message is a reply to:
 Message 10 by Albert de Roos, posted 05-08-2013 6:48 PM Albert de Roos has replied

Replies to this message:
 Message 13 by Albert de Roos, posted 05-09-2013 3:42 AM Pressie has replied

  
NoNukes
Inactive Member


Message 12 of 81 (698707)
05-09-2013 12:33 AM
Reply to: Message 6 by Albert de Roos
05-07-2013 6:17 AM


Classical terms such as natural selection and random mutation seem irrelevant or useless at a macroevolutionary scale.
Could you explain why they would be useless? Is it primarily because it does not fit within your model, or because it is impossible to imagine evolution actually occurring.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615.
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

This message is a reply to:
 Message 6 by Albert de Roos, posted 05-07-2013 6:17 AM Albert de Roos has replied

Replies to this message:
 Message 14 by Albert de Roos, posted 05-09-2013 3:53 AM NoNukes has replied

  
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 13 of 81 (698723)
05-09-2013 3:42 AM
Reply to: Message 11 by Pressie
05-09-2013 12:05 AM


Pressie, I have described my definition of Life in mechanistic terms, and have described viruses as part as other life forms. I use a replicating genome as the definition of Life, so some may consider viruses to be a Life form because they have a genome. I don't see the relevance for the discussion.

This message is a reply to:
 Message 11 by Pressie, posted 05-09-2013 12:05 AM Pressie has replied

Replies to this message:
 Message 15 by Pressie, posted 05-09-2013 4:59 AM Albert de Roos has not replied

  
Albert de Roos
Junior Member (Idle past 3969 days)
Posts: 25
Joined: 05-02-2013


Message 14 of 81 (698724)
05-09-2013 3:53 AM
Reply to: Message 12 by NoNukes
05-09-2013 12:33 AM


Hi NoNukes, the terms random mutation and natural selection are irrelevant for macroevolution because they do not explain the origin of Life, the origin of the cell, the origin of multicellular organisms etc. They also have no mechanistic basis and are non-predictive.
They could well be an important factor in evolution, but irrelevant at the macro level we are talking. In studying the working of an engine, we do not use nanophysics. In order to explain Microsoft XP, we do not use the 0s and 1s, but we talk about software modules and classes.

This message is a reply to:
 Message 12 by NoNukes, posted 05-09-2013 12:33 AM NoNukes has replied

Replies to this message:
 Message 17 by NoNukes, posted 05-09-2013 11:12 PM Albert de Roos has replied

  
Pressie
Member
Posts: 2103
From: Pretoria, SA
Joined: 06-18-2010


Message 15 of 81 (698725)
05-09-2013 4:59 AM
Reply to: Message 13 by Albert de Roos
05-09-2013 3:42 AM


Albert de Roos writes:
Pressie, I have described my definition of Life in mechanistic terms, and have described viruses as part as other life forms. I use a replicating genome as the definition of Life, so some may consider viruses to be a Life form because they have a genome. I don't see the relevance for the discussion.
I completely disagree. It very relevant to discuss what life is in this discussion.

This message is a reply to:
 Message 13 by Albert de Roos, posted 05-09-2013 3:42 AM Albert de Roos has not replied

Replies to this message:
 Message 16 by Genomicus, posted 05-09-2013 2:17 PM Pressie has not replied

  
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