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Author Topic:   Recent paper with an ID spin? Abel and Trevors (2005).
Smooth Operator
Member (Idle past 3458 days)
Posts: 630
Joined: 07-24-2009


Message 46 of 85 (518827)
08-08-2009 4:51 PM
Reply to: Message 45 by Wounded King
08-07-2009 3:48 AM


quote:
They claim you can apply their method to similarly functional but molecularly dissimilar proteins. I think that if they make some claims they should be able to support them with something, I can see how you wouldn't think so though, since you absolutely refuse to support any of your own claims beyond bare repetition.
I always support my claims, but when I get same questions asked over and over again, what else should I do?

quote:
Well have they? Its been 2 and a half years since the paper was published.
Are we talking about the same 2005 paper? Anyway, you have got to give people some time.

This message is a reply to:
 Message 45 by Wounded King, posted 08-07-2009 3:48 AM Wounded King has responded

Replies to this message:
 Message 47 by Wounded King, posted 08-09-2009 5:43 AM Smooth Operator has responded

  
Wounded King
Member (Idle past 2439 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 47 of 85 (518883)
08-09-2009 5:43 AM
Reply to: Message 46 by Smooth Operator
08-08-2009 4:51 PM


I always support my claims, but when I get same questions asked over and over again, what else should I do?

Well, not to put too fine a point on it you should do exactly what you just claimed you do do, but anyone looking at either this thread or the other one about information can see that simply isn't true.

Are we talking about the same 2005 paper? Anyway, you have got to give people some time.

No, we are talking about the 2007 Durston et al. paper that you introduced to the discussion. I understand that it takes time to do research but shouldn't they have done the research before claiming they could do something?

TTFN,

WK

I always support my claims, but when I get same questions asked over and over again, what else should I do?

Well, not to put too fine a point on it you should do exactly what you just claimed you do do, but anyone looking at either this thread or the other one about information can see that simply isn't true.

Are we talking about the same 2005 paper? Anyway, you have got to give people some time.
quote:
They claim you can apply their method to similarly functional but molecularly dissimilar proteins. I think that if they make some claims they should be able to support them with something, I can see how you wouldn't think so though, since you absolutely refuse to support any of your own claims beyond bare repetition.
I always support my claims, but when I get same questions asked over and over again, what else should I do?

Are we talking about the same 2005 paper? Anyway, you have got to give people some time.

No, we are talking about the 2007 Durston et al. paper that you introduced to the discussion. I understand that it takes time to do research but shouldn't they have done the research before claiming they could do something?

TTFN,

WK

Edited by Admin, : Bad quoting, and it Looked like some extraneous material was included so I deleted it. I've included the original version in a hide in case I've fixed this incorrectly, but I had to fix the incorrectly quoted portion, possibly incorrectly.


This message is a reply to:
 Message 46 by Smooth Operator, posted 08-08-2009 4:51 PM Smooth Operator has responded

Replies to this message:
 Message 48 by Smooth Operator, posted 08-19-2009 5:57 PM Wounded King has responded

  
Smooth Operator
Member (Idle past 3458 days)
Posts: 630
Joined: 07-24-2009


Message 48 of 85 (520176)
08-19-2009 5:57 PM
Reply to: Message 47 by Wounded King
08-09-2009 5:43 AM


quote:
Well, not to put too fine a point on it you should do exactly what you just claimed you do do, but anyone looking at either this thread or the other one about information can see that simply isn't true.
So you are saying I never ever posted alink that I used as an argument.

quote:
No, we are talking about the 2007 Durston et al. paper that you introduced to the discussion. I understand that it takes time to do research but shouldn't they have done the research before claiming they could do something?
I thought we were talkign about the 2005 paper. Listen, it's very simple. They know what they are doing. If you have certain problems with their work, than yes, I agree. Nobody's work is perfect. But that doesn't mean it's flat out wrong, and that they can't use the papaer they wrote for anyhting.

This message is a reply to:
 Message 47 by Wounded King, posted 08-09-2009 5:43 AM Wounded King has responded

Replies to this message:
 Message 49 by Wounded King, posted 08-21-2009 6:07 AM Smooth Operator has responded

  
Wounded King
Member (Idle past 2439 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 49 of 85 (520349)
08-21-2009 6:07 AM
Reply to: Message 48 by Smooth Operator
08-19-2009 5:57 PM


So you are saying I never ever posted alink that I used as an argument.

I'm not sure what you are saying here. I don't think you should post a link as an argument, you should be able to make the argument in your own words and use references/links as supporting evidence. You certainly haven't posted links to any supporting evidence in the discussion we have been having on this thread, not since you originally brought up the Durston paper.

Listen, it's very simple. They know what they are doing.

How do you know? How do you know that what they are doing is what they think they are doing? How do you know that they know that they can do what they say they can do?

The way we know these in a scientific paper is because the paper presents the methods and data in such a way that we can know it, barring the possibility of fraud, as well as the author.

But that doesn't mean it's flat out wrong, and that they can't use the papaer they wrote for anyhting.

It doesn't mean that it is right either or that they can use their method for actually doing what they say it can.

Have Durston et al. expanded Abel and Trevor's work to get an algorithm for producing some measure of complexity from sequence alignments, yes but not any better than half a dozen already extant methods. Have they shown how to use this method to analyse a heterogenous set of sequences, no. Have they given us usable criteria for 'Function' that we can use for selection? No.

As far as evidence supportive of ID goes all they have done is assume that they can factor all of these 'FSC' measurements together to get a meaningful overall value for a system or organism. But they give us no reason to assume that this is actually the case along with them. Even if we allow this it only helps ID if we accept it as a measure of probability and further accede to concepts like the 'universal probability bound' being relevant.

TTFN,

WK


This message is a reply to:
 Message 48 by Smooth Operator, posted 08-19-2009 5:57 PM Smooth Operator has responded

Replies to this message:
 Message 50 by Smooth Operator, posted 08-21-2009 8:10 PM Wounded King has responded

  
Smooth Operator
Member (Idle past 3458 days)
Posts: 630
Joined: 07-24-2009


Message 50 of 85 (520515)
08-21-2009 8:10 PM
Reply to: Message 49 by Wounded King
08-21-2009 6:07 AM


quote:
Have Durston et al. expanded Abel and Trevor's work to get an algorithm for producing some measure of complexity from sequence alignments, yes but not any better than half a dozen already extant methods. Have they shown how to use this method to analyse a heterogenous set of sequences, no. Have they given us usable criteria for 'Function' that we can use for selection? No.
Let's see now...

http://www.tbiomed.com/content/supplementary/1742-4682-4-47-s1.rtf

This is their method of computing the FSC. They used the protein sequences from the PFAM database and than they were compared and measured. What do you think is wrong with this method?

quote:
As far as evidence supportive of ID goes all they have done is assume that they can factor all of these 'FSC' measurements together to get a meaningful overall value for a system or organism. But they give us no reason to assume that this is actually the case along with them. Even if we allow this it only helps ID if we accept it as a measure of probability and further accede to concepts like the 'universal probability bound' being relevant.
Why would they not be able to put all those values together? The only reason I could think of is because you think that some of them could have evolved. But could they have done that?

This message is a reply to:
 Message 49 by Wounded King, posted 08-21-2009 6:07 AM Wounded King has responded

Replies to this message:
 Message 51 by AdminNosy, posted 08-21-2009 8:21 PM Smooth Operator has responded
 Message 53 by Wounded King, posted 08-22-2009 4:15 AM Smooth Operator has responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 51 of 85 (520517)
08-21-2009 8:21 PM
Reply to: Message 50 by Smooth Operator
08-21-2009 8:10 PM


bare links again
Let's see you actually explain things in your own words SO. You'll start to get short suspensions if you don't.

This message is a reply to:
 Message 50 by Smooth Operator, posted 08-21-2009 8:10 PM Smooth Operator has responded

Replies to this message:
 Message 52 by Smooth Operator, posted 08-22-2009 12:28 AM AdminNosy has responded

  
Smooth Operator
Member (Idle past 3458 days)
Posts: 630
Joined: 07-24-2009


Message 52 of 85 (520537)
08-22-2009 12:28 AM
Reply to: Message 51 by AdminNosy
08-21-2009 8:21 PM


Re: bare links again
quote:
Let's see you actually explain things in your own words SO. You'll start to get short suspensions if you don't.
I did explain it in short. Am I supposed to explain the whole paper in full details?

This message is a reply to:
 Message 51 by AdminNosy, posted 08-21-2009 8:21 PM AdminNosy has responded

Replies to this message:
 Message 54 by AdminNosy, posted 08-22-2009 9:35 AM Smooth Operator has responded

  
Wounded King
Member (Idle past 2439 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 53 of 85 (520552)
08-22-2009 4:15 AM
Reply to: Message 50 by Smooth Operator
08-21-2009 8:10 PM


This is their method of computing the FSC. They used the protein sequences from the PFAM database and than they were compared and measured. What do you think is wrong with this method?

So where are the usable criteria for function? A PFAM family is based upon structural similarity not function per se. I think the problem with this method is that they claim that it can be used for genes/proteins with similar functions but highly divergent molecular structures, but given their method is based on sequence similarity they give no explanation of how one could do this. Their method seems redundant when compared to more sophisticated metrics like BLOSUM which take into account the physicochemical properties of the amino acids.

Why would they not be able to put all those values together?

Well of course they can. There is nothing creationists and IDers love better than multiplying a whole lot of probabilities together to come up with one really tiny probability and then declaring that it shows evolution is impossible. The question is whether doing so actually has any sort of meaning or utility.

The FSC is really nothing more than a slightly modified measure of conservation. It in no way accounts for all the possible unknown sequences which can also fulfil a particular function. So as usual the probability measurement is only ever going to be for the exact set of genetic structures that have been fed into it. This means that rather than the likelihood of any molecule evolving to perform a particular function you are only looking at the likelihood of the exact molecular set you were studying evolving. So you will no doubt have a very small number but sets of die rolls with infinitesimally small probabilities are generated every day.

TTFN,

WK


This message is a reply to:
 Message 50 by Smooth Operator, posted 08-21-2009 8:10 PM Smooth Operator has responded

Replies to this message:
 Message 64 by Smooth Operator, posted 09-06-2009 9:39 AM Wounded King has responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 54 of 85 (520572)
08-22-2009 9:35 AM
Reply to: Message 52 by Smooth Operator
08-22-2009 12:28 AM


Re: bare links again
This is their method of computing the FSC. They used the protein sequences from the PFAM database and than they were compared and measured. What do you think is wrong with this method?

This is your whole explanation? How were they compared and how measured?

You were replying to:

quote:
Have Durston et al. expanded Abel and Trevor's work to get an algorithm for producing some measure of complexity from sequence alignments, yes but not any better than half a dozen already extant methods. Have they shown how to use this method to analyse a heterogenous set of sequences, no. Have they given us usable criteria for 'Function' that we can use for selection? No.

Where are your words on the method to analyze a heterogeneous set? Where are the usable criteria for function? Either explain them or explain why they aren't needed.

You have apparently already been given what is wrong.


This message is a reply to:
 Message 52 by Smooth Operator, posted 08-22-2009 12:28 AM Smooth Operator has responded

Replies to this message:
 Message 55 by Smooth Operator, posted 08-23-2009 9:12 AM AdminNosy has not yet responded
 Message 65 by Smooth Operator, posted 09-06-2009 9:45 AM AdminNosy has not yet responded

  
Smooth Operator
Member (Idle past 3458 days)
Posts: 630
Joined: 07-24-2009


Message 55 of 85 (520704)
08-23-2009 9:12 AM
Reply to: Message 54 by AdminNosy
08-22-2009 9:35 AM


Re: bare links again
quote:
Where are your words on the method to analyze a heterogeneous set? Where are the usable criteria for function? Either explain them or explain why they aren't needed.
I see, no problem.

I will explain it soon. I'll be back in a week or so when my exams are done. I should really be going to study now.

So, yeah, see you in about a week again...


This message is a reply to:
 Message 54 by AdminNosy, posted 08-22-2009 9:35 AM AdminNosy has not yet responded

  
Wounded King
Member (Idle past 2439 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 56 of 85 (521267)
08-26-2009 5:06 PM


Durston et al . program
I have the Durston et al. programs working with nucleotide sequences as well now. I may tinker a bit more to see if I can get it to accept inputs from the command line rather than needing to modify the core program every time I set up a new analysis.

The Fits profile is moderatley different from the straight conservation profile. In contrast to the protein alignments JalView doesn't have any more sophisticated measures for nucleotide sequences. I might look at some other nucleotide sequence conservation metrics and see what they produce. One interesting methodology is based on DNA topologies allowing higher level DNA structure to influence the detection of conserved regions.

The file link I made previously is broken, I'll see if I can find somewhere stable to put the analysis files.

TTFN,

WK


Replies to this message:
 Message 57 by Percy, posted 08-27-2009 9:52 AM Wounded King has responded

  
Percy
Member
Posts: 19116
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.0


Message 57 of 85 (521385)
08-27-2009 9:52 AM
Reply to: Message 56 by Wounded King
08-26-2009 5:06 PM


Re: Durston et al . program
Isn't the ultimate goal of Durston and company to draw a connection between functional specificity and conscious intent or meaning? And don't they claim that they can detect functional specificity? And wouldn't their measurement technique show high functional specificity for both a real-life protein and an equally long but artificial protein constructed from a random sequence of codons?

In other words, aren't they just making an unsupported claim that complexity is synonymous with meaning?

--Percy


This message is a reply to:
 Message 56 by Wounded King, posted 08-26-2009 5:06 PM Wounded King has responded

Replies to this message:
 Message 58 by Wounded King, posted 08-27-2009 10:20 AM Percy has responded

  
Wounded King
Member (Idle past 2439 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 58 of 85 (521392)
08-27-2009 10:20 AM
Reply to: Message 57 by Percy
08-27-2009 9:52 AM


Re: Durston et al . program
Since their measurement technique is actually based on sequence comparisons the question is rather what would they show for

  • A - A heterogenous set of randomly generated proteins.
  • B - A data set consisting of 1 randomly generated protein compared to itself multiple times.
  • C - A set of sequences all of which are randomly mutated forms of an initial randomly generated sequence.

    They have done one of these (A) as part of their paper ...

    To illustrate the FSC of sequences that only had RSC, an array of 500 uniformly random sequences were generated, each having 1000 sites. The array was input into the software to compute the value in Fits of the FSC of the set of random sequences. To illustrate OSC, the Fit value of a 50-mer sequence of polyadenosine produced on Montmorillonite clay was calculated according to Eqn.

    So they have looked at a set of randomly generated sequences and a single instance consisting of simply 1 repeating polyadenosine poypeptide. It is perhaps important to note that they don't use the same method to compare both, perhaps this is because if you put multiple sets of polyadenosine sequences into their program what actually comes out is that such sequences have a maximal Functional Complexity value.

    They are using Abel and Trevors divisions of sequence complexity into Ordered (OSC), Random (RSC) and Functional (FSC). But they only really seem to be determining conservation with a slight twist. They aren't actually detecting functionality any differently than all the standard bioinformatic methods. They certainly aren't showing they can make meaningful comparisons of a function on the level of 'eye development' rather than 'specific DNA binding site conserved in PFAM family'.

    TTFN,

    WK


  • This message is a reply to:
     Message 57 by Percy, posted 08-27-2009 9:52 AM Percy has responded

    Replies to this message:
     Message 59 by Percy, posted 08-27-2009 11:05 AM Wounded King has responded

      
    Percy
    Member
    Posts: 19116
    From: New Hampshire
    Joined: 12-23-2000
    Member Rating: 3.0


    Message 59 of 85 (521400)
    08-27-2009 11:05 AM
    Reply to: Message 58 by Wounded King
    08-27-2009 10:20 AM


    Re: Durston et al . program
    I guess I'm looking for the connection to ID. Don't they need to compare the FSC of random proteins with real-world proteins of comparable size?

    --Percy


    This message is a reply to:
     Message 58 by Wounded King, posted 08-27-2009 10:20 AM Wounded King has responded

    Replies to this message:
     Message 60 by Wounded King, posted 08-27-2009 11:36 AM Percy has responded

      
    Wounded King
    Member (Idle past 2439 days)
    Posts: 4149
    From: Edinburgh, Scotland
    Joined: 04-09-2003


    Message 60 of 85 (521408)
    08-27-2009 11:36 AM
    Reply to: Message 59 by Percy
    08-27-2009 11:05 AM


    Re: Durston et al . program
    But this doesn't really apply to single proteins. They do compare sets of real world proteins, their PFAM analyses, with sets of randomly generated proteins of roughly similar length. Naturally the set of randomly generated proteins has much less FCS/conservation than the PFAM families, see Table 1 in Durston et al. (2007). But this isn't because ofthe magic of ID, its because of conservation and all the work PFAM has done categorising and aligning structurally related protein families.

    TTFN,

    WK

    Edited by Wounded King, : No reason given.

    Edited by Wounded King, : No reason given.

    Edited by Wounded King, : No reason given.


    This message is a reply to:
     Message 59 by Percy, posted 08-27-2009 11:05 AM Percy has responded

    Replies to this message:
     Message 61 by Percy, posted 08-27-2009 2:20 PM Wounded King has responded

      
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