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Author Topic:   An ID hypothesis: Front-loaded Evolution
ScientificBob
Member (Idle past 3577 days)
Posts: 48
From: Antwerp, Belgium
Joined: 03-29-2011


Message 91 of 216 (653599)
02-23-2012 1:55 AM
Reply to: Message 1 by Genomicus
02-19-2012 5:43 AM


I think it's funny how you assume "intent" in your "hypothesis", while "intent" is exactly what cdesign proponentsists are trying to conclude.

"I assume there was intent so therefor, there was".


This message is a reply to:
 Message 1 by Genomicus, posted 02-19-2012 5:43 AM Genomicus has not replied

  
Wounded King
Member (Idle past 3409 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 92 of 216 (653616)
02-23-2012 5:03 AM
Reply to: Message 84 by jar
02-22-2012 11:15 AM


Re: The best of error minimizing codes?
I'm not quite sure what you are asking about here Jar. The question of universality which your quote from Freeland addressed is pretty clear, there is no 'Universal' genetic code but there is one that is by far the most prevalent standard.

That is a very distinct question to the one the paper I referenced addressed towards the optimality of the standard genetic code. In fact the Freeland paper you referenced doesn't really say much about code optimisation at all.

TTFN,

WK


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 Message 84 by jar, posted 02-22-2012 11:15 AM jar has replied

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Dr Jack
Member (Idle past 1419 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 93 of 216 (653619)
02-23-2012 5:31 AM


Catching up
I've not been able to post in a while, and I see the thread has moved on a bit since I last posted. Rather than attempting to pick up dropped threads I think it's probably best if I make a more general reply to recent points. Genomicus: if there's any particular point you made in your responses to you that I've not responded to and you would like addressed, please feel free to raise it again and I'll answer it as best I can.

On the genomes of bacteria and the need for fidelity

I raise objection to your claim that bacteria should be more resistant to mutation and should benefit from more rapid mutation. In fact, both are likely untrue. The first reason to suspect this is straightforwardly empirical - error rates are lower in prokaryotic DNA replication mechanisms. Bacteria carry mutations at a lower rate than humans, and other other higher animals*.

The second reason is more theoretical: bacterial genomes are simply less redundant. Whereas animals tend to be diploid (they have two copies of each gene), prokaryotes are universally haploid (they have one copy of each gene): this means that any error is always expressed in prokaryotes whereas animals typically have another copy around to pick up the slack. Multi-cellularity also provides a further line of support because alterations expressed only in a certain cell type can drag down only that particular cell type and the rest of the organisms may be able to support that; single-celled organisms must function on their own. This also applies to environmentally relevant adaptations - a horse that can't suggest a certain plant can typically find a different plant to eat, whereas a lactose-metabolism deficient bacterium is stuck in its environment. Finally, the molecular pathways of multi-cellular organisms typically contain some redundancy, whereas bacterial molecular pathways are generally much more tightly regulated and the loss of single parts is more likely to destroy entire pathways.

On Pax6

In Message 64, you said:

Genomicus writes:

Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.

Did you carry out this BLAST yourself? Can you give more precise details on what you did? I have just attempted to repeat your BLAST to have a look at what is matching, but when I performed a blast with the European Bioinformatics Institute against their databases of Baceria and Archaea, I found no significant matches (link valid for 7 days, apparently). A similar search carried out using UniProt produced similar results - even the high E value results I did found matched simply in a high Pro/Ser/Thr-region which is unlikely to have profound biological significance.

Could you link to your results? Or, if you did not search yourself, perhaps you could identify your source?

As an aside I'd note that I would usually simply ignore any hits from BLAST with E-values as high as 1e-05 as simple noise; although I concede that deep-relationship searches must - by necessity - work with less-similar proteins.

* - Rapid-mutation mechanisms such as phase variation, and stress-response mechanisms - if they exist - aside.

Edited by Mr Jack, : No reason given.


Replies to this message:
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Wounded King
Member (Idle past 3409 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 94 of 216 (653622)
02-23-2012 6:42 AM
Reply to: Message 93 by Dr Jack
02-23-2012 5:31 AM


Re: Catching up
I just performed the same search, on the NCBI site limiting the search to the Prokaryota, and there were indeed hits below the 1e-05 level, a grand total of three of them and all from the same thing, a putative paired box domain protein from the protobacteria Methylocystis. I imagine that the sequence similarity is why this is identified as a putative paired box domain protein in the first place.

The region that comes up only covers 23% of the submitted amino acid sequence and has a maximum identity of 30% and less than 50% for positive (BLOSUM62 compatible) sites. If this was what he got then I'm not surprised Genomicus didn't want to go into any more detail about the results since they are so weak.

Perhaps more relevantly all of the lower hits are from tranposon and insertion sequences, suggesting that what we are seeing is a convergent signature for DNA binding interacting activity rather than an ancestral relic of a front loaded primeval PAX gene lineage. To support this the SMART database of protein architecture identifies 3 bacterial hits for the PAX domain and all 3 are from transposase sequences.

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 93 by Dr Jack, posted 02-23-2012 5:31 AM Dr Jack has replied

Replies to this message:
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Chuck77
Inactive Member


(1)
Message 95 of 216 (653623)
02-23-2012 6:56 AM


A summary
I wish I could help Genomicus but i've read thru some recent pages and am quite lost. He's being bombarded pretty good by lots of people and he's new.

Can anyone someone lay his position out for me in laymans terms? Is he arguing that evolution was front loaded by a creator/deity?

Or is he arguing for the IDist POV along with the likes of Behe and Meyer?

Like I said this above my pay grade especially the last few posts by Mr Jack and Wounded King so if someone has the time can you summarize his position for me, it's to complicated from the various posts.

Not that i'm going to be able to help him but maybe provide some support somehow if I understand it more. Thanks.

Edited by Chuck77, : No reason given.


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Dr Jack
Member (Idle past 1419 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 96 of 216 (653626)
02-23-2012 7:34 AM
Reply to: Message 94 by Wounded King
02-23-2012 6:42 AM


Re: Catching up
Ah, found it. Thank you, Wounded King.

This message is a reply to:
 Message 94 by Wounded King, posted 02-23-2012 6:42 AM Wounded King has replied

Replies to this message:
 Message 101 by Wounded King, posted 02-23-2012 11:35 AM Dr Jack has replied

  
Theodoric
Member
Posts: 7411
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 2.7


(2)
Message 97 of 216 (653628)
02-23-2012 8:13 AM
Reply to: Message 95 by Chuck77
02-23-2012 6:56 AM


Re: A summary
I wish I could help Genomicus but i've read thru some recent pages and am quite lost. He's being bombarded pretty good by lots of people and he's new.

Can anyone someone lay his position out for me in laymans terms? Is he arguing that evolution was front loaded by a creator/deity?

Or is he arguing for the IDist POV along with the likes of Behe and Meyer?

Like I said this above my pay grade especially the last few posts by Mr Jack and Wounded King so if someone has the time can you summarize his position for me, it's to complicated from the various posts.

Not that i'm going to be able to help him but maybe provide some support somehow if I understand it more. Thanks.

A reasonable person would stay out of a debate if he does not understand it or if the subject matter is beyond their grasp. You will notice that most "evolutionists" here are staying out of the debate.

I find it amazing that you want to support Geno, solely because he has a theistic argument. You do not care if his argument is correct, but it must be because it is theistic. That is disgusting.

Oh for just one honest Creo.


Facts don't lie or have an agenda. Facts are just facts

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crashfrog
Member (Idle past 781 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 98 of 216 (653629)
02-23-2012 8:19 AM
Reply to: Message 95 by Chuck77
02-23-2012 6:56 AM


Re: A summary
Asking for clarification is no sin, but it would help if you posed more specific questions about what you didn't understand.

This message is a reply to:
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jar
Member
Posts: 33957
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.2


Message 99 of 216 (653634)
02-23-2012 9:10 AM
Reply to: Message 92 by Wounded King
02-23-2012 5:03 AM


Re: The best of error minimizing codes?
Does it go into how and why the standard code evolves over time?

Anyone so limited that they can only spell a word one way is severely handicapped!

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Granny Magda
Member (Idle past 149 days)
Posts: 2384
From: UK
Joined: 11-12-2007


Message 100 of 216 (653641)
02-23-2012 10:53 AM
Reply to: Message 95 by Chuck77
02-23-2012 6:56 AM


Re: A summary
Hi Chuck,

Can anyone someone lay his position out for me in laymans terms? Is he arguing that evolution was front loaded by a creator/deity?

Or is he arguing for the IDist POV along with the likes of Behe and Meyer?

Well if I remember correctly, Behe goes as far as to say that he suspects the designer to be the Christian god. Certainly Genomicus doesn't go that far. If you take a look at his blog, particularly this post, he expresses his frustration at many within ID over their insistence on dragging theism into the mix. He sees this - quite correctly - as being counter to good science. Here's a quote;

quote:
When I look at the posts over at UncommonDescent, it is obvious to me that a change needs to occur within the mainstream ID team. At least 50% of the posts at UncommonDescent, aren’t even remotely relevant to ID and biological origins (well, I suppose by some stretch of the imagination they could be just a tiny, tiny bit relevant). Consider the title of one of the posts at UncommonDescent: “Survey results: Only 5.3% of general philosophers of science accept or lean towards theism.” Now what on earth does theism have to do with biological intelligent design? I really don’t know. Does theism have anything to do with the theory of gravity? Not really, and if the mainstream proponents of ID are genuinely interested in developing a rigorous hypothesis of biological origins, then the theistic language will have to be dropped (or at least minimized). I mean, c’mon, UncommonDescent spends a whole bunch of time devoted to attacking atheism, promoting theism, etc. But what does this have to do with the origin of the bacterial flagellum, for example? If you’re truly interested in biological origins, then we don’t need to be sidetracked by the theism/atheism debate, which is a whole other topic.

Now I come close to agreeing with him here. ID is indeed far too steeped in religion. Where I differ from Genomicus' position is in his view that "theistic language" is what needs to minimised in ID. I think that's wrong. I think that the real problem is not merely theistic language, but the whole focus of ID. The problem is not that the posters at Uncommon Descent have misunderstood the point of ID, it's that Genomicus has misunderstood the point. That point is that ID exists solely for the purpose of Christian apologetics, specifically, getting those apologetics into schools. It's not just the language, it's the whole ideology.

For ID to produce the kind of good science that Genomicus seems to honestly desire, it would have to abandon it's dishonest approach to the subject. It would have to become something totally different to what it is today. It would have to drop it's political and religious aims and concentrate solely on the data. But then of course, it would no longer be ID science, it would just be science.

This is another topic I admit, but it might make an interesting thread when we've finished with this one.

If you want more on the science side of things, check out Genomicus' blog. It's quite good as these things go and it has a lot of material on this subject. I still don't think he's right, but it should be of interest to you.

Mutate and Survive


This message is a reply to:
 Message 95 by Chuck77, posted 02-23-2012 6:56 AM Chuck77 has replied

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Wounded King
Member (Idle past 3409 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 101 of 216 (653652)
02-23-2012 11:35 AM
Reply to: Message 96 by Dr Jack
02-23-2012 7:34 AM


DNA / Protein disjunction
On another related point, if you take the mRNA coding for the sequence that Genomicus chose and blast that against the Prokaryota then you get no significant hits. As with the prestin gene the convergence at the amino acid sequence level does not extend to the DNA sequence, rather undecutting the contention that these reflect a deep ancestral genetic sequence.

In fact I was surprised not to get any significant hits since you would expect the selection for the similar amino acid sequences to produce some convergence, as there was some evidence for in the prestin paper, then again that similarity itself is so low that once the degeneracy of the genetic code is factored in perhaps there is no reason to expect any significant similarity at the DNA level.

And I'm not even going to start pointing out how massively unlikely such a handful of hits, especially ones so minimally below the significance level, is to support the sort of scenario Genomicus outlines when the sequences seem to be missing from the vast majority of all other prokaryotes.

Once again as with the prestin example if you take out virtually all the other context and cherry pick your organisms you can produce what look like highly unlikely convergences. But if you look below the amino acid level and include a wider panel of organisms the proposed examples of some sort of programmed genetic response become nothing but smoke on the wind.

TTFN,

WK


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 Message 96 by Dr Jack, posted 02-23-2012 7:34 AM Dr Jack has replied

Replies to this message:
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Panda
Member (Idle past 3027 days)
Posts: 2688
From: UK
Joined: 10-04-2010


(1)
Message 102 of 216 (653657)
02-23-2012 12:02 PM
Reply to: Message 97 by Theodoric
02-23-2012 8:13 AM


Re: A summary
Thoedoric writes:

I find it amazing that you want to support Geno, solely because he has a theistic argument. You do not care if his argument is correct, but it must be because it is theistic. That is disgusting.


Which is ironic since Geno is not presenting a theistic argument.
His argument appears (to me) to be agnostic.

If I were you
And I wish that I were you
All the things I'd do
To make myself turn blue

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Theodoric
Member
Posts: 7411
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 2.7


Message 103 of 216 (653663)
02-23-2012 12:46 PM
Reply to: Message 102 by Panda
02-23-2012 12:02 PM


Re: A summary
On its face ID is Theistic.

Facts don't lie or have an agenda. Facts are just facts

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Perdition
Member (Idle past 2552 days)
Posts: 1593
From: Wisconsin
Joined: 05-15-2003


Message 104 of 216 (653684)
02-23-2012 3:17 PM
Reply to: Message 95 by Chuck77
02-23-2012 6:56 AM


The Blind leading The Blind
Chuck asked for a layman's explanation of Genomicus' position, and who better to do that than another layman? If this should be spun off into a Peanut Gallery thread, or even just a new parallel thread, I'd be happy to do that as well. As I said, I'm a layman, and though I think I understand the gist of what everyone is saying, any points I get wrong are due to my own misunderstanding, and corrections are welcome.

Essentially, Genomicus seems to be saying that evolution, as we know and love it, is correct, but is not the whole picture. He seems to think that some undefined designer created the first living creature with DNA that contained the instructions for functions or organs that would be necessary in the future, but that were not necessary at the time. (In other words, these functions were front-loaded.)

There seems to be two major issues with this idea that have been brought up by many posters on this thread. Now, before anyone accuses the evolutionists of being unfair to Genomicus, I feel I should point out that this is how science works. When someone has a new idea, it gets proposed, then the rest of the scientific community tries to tear the idea a new one. If the person who proposed the hypothesis (not theory) cannot answer these problems, either the hypothesis is wrong, and needs to be either changed or thrown out, or the proposer does not sufficiently understand the proposal or the consequences of the proposal. Either way, the proposer needs to go back and do more work.

The two problems in Genomicus' hypothesis are, basically, 1) mutation and 2) verification.

1) He admits that most of evolution happens via mutation and natural selection. The problem is, what mechanism does he propose that would shield these front-loaded genes, or protogenes from mutations that would make them unusable in the thousands or millions of years before they are needed? Secondly, does he have any evidence for this mechanism?

He seems to try to get around this issue by saying that these protogenes would do something different in the original life forms until they are changed to do what they are needed to do in later life. Again, by what mechanism does the geneome ensure the right mutation to change the gene in question, at the right time, to make it do the funtion it was front0loaded for, and does he have any evidence for it?

2) The second problem is verification. For a new hypothesis to be taken seriously, it needs to predict something that an established theory doesn't. So far, everything he's proposed support his idea and evolution as we know it equally well. What he needs is something that evolution doesn't predict, and can't be explained by a slight tweaking of evolutionary theory.

It doesn't matter which order Genomicus answers the two problems listed above, because either one of them, unanswered, is enough to discount the idea, however, it would seem that solving problem one (finding a mechanism to avoid or direct mutation) would solve problem two.

Is this a sufficiently "layman" description, and perhaps more importantly, am I correct in my basic description of the debate?


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Replies to this message:
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Tangle
Member
Posts: 8579
From: UK
Joined: 10-07-2011
Member Rating: 2.9


Message 105 of 216 (653686)
02-23-2012 3:34 PM


It seems to me that 'front loaded' is the wrong terms. What is actually meant is pre-programmed or predetermined.

Life, don't talk to me about life - Marvin the Paranoid Android

  
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