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Author Topic:   What's the problem with teaching ID?
Genomicus
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Joined: 02-15-2012
Member Rating: 3.4


Message 316 of 337 (665058)
06-07-2012 2:35 PM
Reply to: Message 309 by Taq
06-07-2012 2:11 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
What evidence led you to this conclusion?

If you will recall, I've discussed my views on a thread on this site some months ago. I have no intention of re-hashing our discussion here.

Not really. Archael flagella are non-homologous, so it would appear that the two motility systems evolved independently in bacteria and archae.

Alternatively, the original cells seeded on earth was a pool of different Bacteria and Archaea phyla, which means that the Bacteria would have their own flagella, and Archaea would have theirs. Another possibility is that the LUCA had both bacterial and archaeal flagella.

Sure we can. Secretory systems and flagella share a common system which can be traced using sequence comparisons:

Aside from citing a ghastly paper that messed up badly in bioinformatics, let me respond to your argument in brief.

It is quite true that the flagellar motor proteins MotAB share homology with TolQR of the Tol-pal system. However, there are several possibilities here. Firstly, the Tol-pal system might be more ancient than the flagellum; secondly, the two might share a common non-flagellar ancestor; and thirdly the Tol-pal system might be derived from the flagellar motor proteins. The homologous nature of the two systems does not tell us their real evolutionary history.

The origin of the TTSS is a matter of debate, with some researchers arguing that the TTSS evolved from the flagellar secretory apparatus and others arguing that the two share a common ancestor in the form of an export system.

Various arguments have been put forward in favor of the view that the TTSS evolved directly from the flagellar system. While flagellar systems are found in both gram-negative and gram-positive bacteria (Saier, 2004), the TTSS seems to be restricted to gram-negative bacteria, and are found only in Proteobacteria (Saier, 2004; Hueck, 1998) and Chlamydiales (Kim, 2001). In contrast, flagellar systems are found in deep-branching eubacteria such as Thermotoga and Aquifex. Further, the bacterial flagellum is present in the Firmicutes, also deep-branching bacteria (Ciccarelli et al., 2006). That flagellar systems are found in deep-branching bacteria while TTSSs are limited to late-branching bacteria is a direct confirmation of a prediction of the hypothesis that the TTSS is derived from the flagellar system: namely, that the flagellum would be the more ancient of the two systems.

Gophna et al. (2003) countered this argument, noting that structural constraints on the TTSS requires that it be associated only with gram-negative bacteria, which have two membrane envelopes instead of one. However, Saier (2004) responded that flagellar systems have been able to adapt to both gram-negative and gram-positive bacteria, while the TTSS has not, and concludes that the most plausible explanation for this observation is that the TTSS arose in pre-existing gram-negative bacteria, considerably later than flagellar systems.

Phylogenetic research has not resolved the question of the origin of the TTSS, and results derived from such studies have been the subject of different interpretations. Based on branch lengths of phylogenetic trees of TTSS and flagellar protein sequences, Gophna et al. (2003) concluded that TTSS sequences are as ancient as the flagellar proteins. However, branch lengths merely indicate degree of sequence divergence (Pao et al., 1998; Saier, 2004), and different protein families are known to have evolved at varying rates (Smith and Doolittle, 1992; Pagel, 1999; Saier, 2004). Saier (2004) notes that establishing pathogenic or symbiotic associations with different eukaryotic hosts would require different types of substrate proteins, and this would presumably increase the degree of TTSS sequence divergence relative to flagellar systems. Thus, there is the very real possibility that TTSS protein sequences have diverged at a faster rate than flagellar proteins. This possibility is especially realistic when one considers that, in general, orthologous genes diverge at slower rates than laterally transferred genes, and TTSS genes have been extensively transferred laterally, unlike flagellar genes.

Also, when you look at Gophna et al.'s (2003) FliI/SctN tree, you'll see that SctN actually nests within the flagellar FliI protein. This is interesting because FliI/SctN are the most conserved proteins among the two systems, which implies that they should best reflect the true phylogenetic history of the TTSS. As a more minor point, it should be pointed out that 3 out of 4 phylogenies constructed by Gophna et al. are not supported by statistically significant bootstrap values.

Quite contrary to the paper you cite, the homology the TTSS shares with flagella is not at all a clear indicator that the flagellar system originated as a secretory system. The citation the paper uses to support the statement that "The structural features of the flagellum, along with the evidence of homology between FliI and ATP synthase subunits and between MotA/B and the secretion proteins TolQ-TolR, suggests that it originated as a primitive secretion system" isn't a peer-reviewed source AFAIK.

References

Saier M. (2004) Evolution of bacterial type III protein secretion systems. Trends in Microbiology 12(3):113-115.

Hueck CJ. (1998) Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants. Microbiol Mol Biol Rev. 62:379-433.

Kim JF. (2001) Revisiting the chlamydial type III protein secretion system: clues to the origin of type III protein secretion. Trends Genet. 17(2):65-69.

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287.

Gophna U, Ron E, Graur D. (2003) Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312:151-163.

Pao SS, Paulsen IT, Saier MH, Jr. (1998) Major Facilitator Superfamily. Microbiol Mol Biol Rev. 62(1):1-34.

Smith MW, Doolittle RF. (1992) A comparison of evolutionary rates of the two major kinds of superoxide dismutase. J Mol Evol. 34:175184.

Pagel M. (1999) Inferring the historical patterns of biological evolution. Nature 401:877884.


This message is a reply to:
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Genomicus
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Posts: 844
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Member Rating: 3.4


Message 317 of 337 (665060)
06-07-2012 2:40 PM
Reply to: Message 314 by Taq
06-07-2012 2:22 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Actually, it's not. SETI is looking for a narrowband radiowave transmission. Whether SETI is able to discern any analog or binary embedded code is secondary. What they are looking for is a very narrowband signal that looks like this:

And you're still missing the point. The principle of detecting design is the same. You nailed it right here:

Because no known astronomical process produces narrowband signals. They produce broadband signals.

Similarly, ID proponents are trying to demonstrate that certain biological system cannot be produce by any known non-telic process. Whether they have succeeded at that, is, of course, an entirely different matter.


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 Message 314 by Taq, posted 06-07-2012 2:22 PM Taq has responded

Replies to this message:
 Message 321 by Taq, posted 06-07-2012 3:56 PM Genomicus has responded

  
Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 318 of 337 (665061)
06-07-2012 2:42 PM
Reply to: Message 315 by Taq
06-07-2012 2:25 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Can you give an example of a functional protein that shares deep homology amongst eukaryotes which is also unnecessary?

Read what I said again, then come back and ask your question:

However, I argued in that article why the front-loading hypothesis requires that eukaryotic proteins share deep homology with unnecessary but functional prokaryotic proteins.

I should add that by "unnecessary" I mean a protein that is not necessary to the existence of life.


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Replies to this message:
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NoNukes
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Posts: 9657
From: Central NC USA
Joined: 08-13-2010
Member Rating: 3.2


Message 319 of 337 (665065)
06-07-2012 3:28 PM
Reply to: Message 310 by Genomicus
06-07-2012 2:13 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
However, I argued in that article why the front-loading hypothesis requires that eukaryotic proteins share deep homology with unnecessary but functional prokaryotic proteins. Front-loading basically would not work if we did not see this.

I don't understand why you think this makes your argument more convincing.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison


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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 320 of 337 (665066)
06-07-2012 3:32 PM
Reply to: Message 319 by NoNukes
06-07-2012 3:28 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Err, because one model (FLH) is making a prediction, while another model (modern synthesis) is merely capable of explaining an observation. So it all boils down to whether you're an "explanationist" or a "predictionist": which one do you lend more weight to? And it's not like philosophers of science are in agreement on this - I'll grant you that.
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Taq
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Posts: 6648
Joined: 03-06-2009
Member Rating: 4.1


Message 321 of 337 (665068)
06-07-2012 3:56 PM
Reply to: Message 317 by Genomicus
06-07-2012 2:40 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Similarly, ID proponents are trying to demonstrate that certain biological system cannot be produce by any known non-telic process.

And where have they done this?

Whether they have succeeded at that, is, of course, an entirely different matter.

It would seem to be germane to the topic. If they have not then ID is not a subject worth teaching. As it is, we observe all life evolving through natural mechanisms, and we have evidence that these mechanisms were operating in the past. This would be equivalent to SETI finding broadband signals from naturally occuring processes.


This message is a reply to:
 Message 317 by Genomicus, posted 06-07-2012 2:40 PM Genomicus has responded

Replies to this message:
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Taq
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Posts: 6648
Joined: 03-06-2009
Member Rating: 4.1


Message 322 of 337 (665069)
06-07-2012 3:57 PM
Reply to: Message 320 by Genomicus
06-07-2012 3:32 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Err, because one model (FLH) is making a prediction,

A prediction that seems to be a contradiction. You point to proteins that have function and at the same time want to claim that they are useless. Those two things do not go together.


This message is a reply to:
 Message 320 by Genomicus, posted 06-07-2012 3:32 PM Genomicus has responded

Replies to this message:
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Taq
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Posts: 6648
Joined: 03-06-2009
Member Rating: 4.1


Message 323 of 337 (665070)
06-07-2012 4:01 PM
Reply to: Message 318 by Genomicus
06-07-2012 2:42 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
I should add that by "unnecessary" I mean a protein that is not necessary to the existence of life.

Then FLH is making the same prediction as evolution. If a protein produces a competitive advantage to an organism then it will be selected for, even if that protein is not necessary for the existence of life.

For example, a bacterium can survive without a flagellum. However, it will be outcompeted by flagellated bacteria if motility is an advantage.

Therefore, FLH does not distinguish itself from natural mechanisms. Using the SETI example, you are claiming that broadband signals identical to naturally produced signals are in fact designed. You are not using the SETI model.


This message is a reply to:
 Message 318 by Genomicus, posted 06-07-2012 2:42 PM Genomicus has responded

Replies to this message:
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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 324 of 337 (665075)
06-07-2012 4:43 PM
Reply to: Message 321 by Taq
06-07-2012 3:56 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
If they have not then ID is not a subject worth teaching.

Of course, if you had followed this thread you would know that I don't advocate the teaching of ID in school.


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Replies to this message:
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Genomicus
Member
Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 325 of 337 (665076)
06-07-2012 4:47 PM
Reply to: Message 322 by Taq
06-07-2012 3:57 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
You point to proteins that have function and at the same time want to claim that they are useless. Those two things do not go together.

You can have a protein that is functional but deleting it won't kill the organism, or even significantly reduce its fitness, which means it's not necessary for life. I never, ever, ever said anything about a protein that is both functional and useless. You're putting words into my mouth Taq.


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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 326 of 337 (665077)
06-07-2012 4:47 PM
Reply to: Message 323 by Taq
06-07-2012 4:01 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Then FLH is making the same prediction as evolution.

No. See here:
http://thegenomestale.wordpress.com/...ogy-and-front-loading


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Replies to this message:
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Dr Adequate
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Posts: 15942
Joined: 07-20-2006
Member Rating: 3.3


Message 327 of 337 (665079)
06-07-2012 5:05 PM
Reply to: Message 324 by Genomicus
06-07-2012 4:43 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Of course, if you had followed this thread you would know that I don't advocate the teaching of ID in school.

That is what the thread's about; you can hardly get snippy with Taq for supposing that your posts were intended to relate in some way to the topic.


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PaulK
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Posts: 12772
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Member Rating: 3.0


Message 328 of 337 (665080)
06-07-2012 5:06 PM
Reply to: Message 326 by Genomicus
06-07-2012 4:47 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
The argument doesn't make a lot of sense to me.

Why would the LUCA have a minimal set of genes ? Wouldn't it be expected to have more than the absolute minimum ? Given evolution, rather than design.

Secondly even if you could argue that the LUCA would have a minimal set of genes, don't you need to show that the genes you refer to ARE from the LUCA and AREN'T part of a minimal set or derived from a minimal set ? I don't see any argument to that effect.

Also, suppose that the LUCA DID have a minimal set of genes and they DID allow for the evolution of modern life as we see it. Wouldn't that be an even better argument for front-loading ? And if that is true how can a non-minimal gene set in the LUCA be a prediction of front-loading ?

Finally, the argument that non-teleological evolution wouldn't plan for the things we see is only useful if you can show evidence of planning for the things that we see today. Otherwise it really is a "the designer loves giraffes" argument.


This message is a reply to:
 Message 326 by Genomicus, posted 06-07-2012 4:47 PM Genomicus has responded

Replies to this message:
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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 329 of 337 (665082)
06-07-2012 5:18 PM
Reply to: Message 328 by PaulK
06-07-2012 5:06 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Why would the LUCA have a minimal set of genes ? Wouldn't it be expected to have more than the absolute minimum ? Given evolution, rather than design.

No, because the LUCA could easily have been a simple progenote (and, indeed, a number of papers have argued for this, which kinda indicates evolution doesn't predict a progenote or a non-progenote for LUCA), and, actually, the LUCA could have been a simple self-replicating molecule encoding only a few genes. A population of these self-replicators could then have branched off, eventually forming into the domains of life that we see today.

Secondly even if you could argue that the LUCA would have a minimal set of genes, don't you need to show that the genes you refer to ARE from the LUCA and AREN'T part of a minimal set or derived from a minimal set ?

Yes, of course. To determine that they aren't part of a minimal set, you need to do homology comparisons.

Also, suppose that the LUCA DID have a minimal set of genes and they DID allow for the evolution of modern life as we see it. Wouldn't that be an even better argument for front-loading ?

Huh? I have no idea where you're going with this.

Finally, the argument that non-teleological evolution wouldn't plan for the things we see...

That's not my argument. I'm simply pointing out that the FLH makes a specific prediction which non-teleological evolution does not make. And it's not a case of "the designer wanted giraffe's" any more than evolutionary predictions are like that.


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 Message 328 by PaulK, posted 06-07-2012 5:06 PM PaulK has responded

Replies to this message:
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 Message 332 by Dr Adequate, posted 06-07-2012 6:14 PM Genomicus has responded

  
PaulK
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Posts: 12772
Joined: 01-10-2003
Member Rating: 3.0


Message 330 of 337 (665085)
06-07-2012 5:48 PM
Reply to: Message 329 by Genomicus
06-07-2012 5:18 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
quote:

No, because the LUCA could easily have been a simple progenote (and, indeed, a number of papers have argued for this, which kinda indicates evolution doesn't predict a progenote or a non-progenote for LUCA), and, actually, the LUCA could have been a simple self-replicating molecule encoding only a few genes. A population of these self-replicators could then have branched off, eventually forming into the domains of life that we see today.

However, whatever it was, it would not be expected to have a minimal gene set for whatever it was, would it ? Simplicity is more an aim of design rather than evolution. Once evolution gets going we should expect more complexity than is strictly needed.

Come to that, isn't it also argued that there was a large amount of horizontal gene transfer in the early stages of life ? In that case we wouldn't be dealing with the genes for just one organism at all, We would have to consider every gene in every organism.

quote:

Yes, of course. To determine that they aren't part of a minimal set, you need to do homology comparisons.

Isn't your argument that there genes going back to the LUCA which are NOT part of a minimal set ? Surely homology tests will - at most - show if the LUCA likely had a homologous gene or not ?

quote:

Huh? I have no idea where you're going with this.

Suppose that rather than there being NO minimal gene sets that allowed for the evolution of life that we see today there were a VERY FEW - a very small proportion - that did. Wouldn't then, a LUCA with one of those gene-sets be entirely compatible with the concept of front-loading ?

quote:

That's not my argument. I'm simply pointing out that the FLH makes a specific prediction which non-teleological evolution does not make. And it's not a case of "the designer wanted giraffe's" any more than evolutionary predictions are like that.

For it to be a prediction, you have to show that a minimal gene set doesn't provide the flexibility needed - especially given the time available - and you haven't done that.


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