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Author Topic:   What's the problem with teaching ID?
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 286 of 337 (665004)
06-07-2012 12:18 AM
Reply to: Message 284 by Genomicus
06-06-2012 11:56 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Allow me to elaborate. The modern synthesis might be able to explain some biological feature, while an ID hypothesis would predict that biological feature. If the prediction is confirmed, this is evidence for that ID hypothesis, regardless of whether non-telic evolution can explain it or not. Science is built upon a track record of successful predictions, not on whether some alternative model can explain the feature under consideration.
Consider the following example. Evolution predicts that if the bacterial flagellum evolved, a number of its components will share similarity with proteins that are more ancient than the bacterial flagellum. Can the hypothesis that the flagellum was engineered explain this? Yes. Engineers very often re-use parts in different systems. But the ID hypothesis does not predict that the flagellar components will share similarity with more ancient proteins. This is because engineers can also design from scratch. So, while ID can explain this, it does not predict it. Which means that, when it comes to similarity, evolution is the superior explanation (note that the similarity flagellar components share with other proteins is not incompatible with the hypothesis that it was engineered).

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Replies to this message:
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 Message 293 by Drosophilla, posted 06-07-2012 8:20 AM Genomicus has replied

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


Message 287 of 337 (665005)
06-07-2012 12:21 AM
Reply to: Message 285 by Dr Adequate
06-07-2012 12:15 AM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
If evolution can explain something happening, it also predicts that it can happen. If it can happen under an evolutionary hypothesis, then it is not unique to an ID hypothesis.
See my response to this (I wrote the response before I saw this comment of yours, so read in context).
What you just said is just as philosophically sound as saying that "since the hypothesis that the flagellum was engineered can explain the similarity flagellar proteins share with other non-flagellar proteins, this means that the engineering hypothesis predicts that flagellar proteins share will share with other non-flagellar proteins."

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 Message 285 by Dr Adequate, posted 06-07-2012 12:15 AM Dr Adequate has replied

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


Message 289 of 337 (665007)
06-07-2012 12:31 AM
Reply to: Message 288 by Dr Adequate
06-07-2012 12:27 AM


Re: ID Predictions
Let's focus on one thing at a time Dr Adequate, if you don't mind (not at all trying to evade your point, just trying to prevent us from going 'round and 'round in circles ).
Do you agree that if an ID hypothesis necessarily predicts biological feature X, while evolutionary theory only explains it, then confirmation of that prediction is a chunk of data in favor of the ID hypothesis?
Edited by Genomicus, : No reason given.
Edited by Genomicus, : No reason given.

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


Message 294 of 337 (665032)
06-07-2012 10:25 AM
Reply to: Message 291 by Dr Adequate
06-07-2012 12:44 AM


Re: ID Predictions
Well, that would depend. Take my example of a Designer who is really keen on giraffes. This would predict giraffes, whereas evolution would only explain them. Nonetheless, this isn't really evidence in favor of the hypothesis of a giraffophile Designer.
Well, such a hypothesis of a designer (why on earth do you capitalize designer?) who is keen on giraffe's would have been inspired by the existence of giraffes, so you couldn't predict the existence of giraffes precisely because they already exist. Now, if we were living on Mars, instead of on Earth, and using teleology (I don't know how this would work) we predicted that giraffe-like animals would be found on earth, and we found that this was indeed the case, it would be evidence for the telic hypothesis.

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


Message 295 of 337 (665033)
06-07-2012 10:28 AM
Reply to: Message 293 by Drosophilla
06-07-2012 8:20 AM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
But to the best of my knowledge, designers (human ones at least) don't re-use parts in dangerous configurations. Which fool decided that we should have a food pipe and a breathing pipe so connected to allow a choking option.
I'm a proponent of the ID hypothesis of front-loading, wherein eukaryotes, Metazoa, plants, and other "higher" taxa were front-loaded from genomes that were engineered and delivered to earth via directed panspermia. So I don't think humans were specifically engineered.
The bacterial flagellum is a different case because (a) it is found in basal bacterial lineages, which means it could have been present in the LUCA, and therefore directly engineered, and (b) I don't think you're going to find the molecular equivalent of the backward wiring of the eye in the core flagellar structure.

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


Message 296 of 337 (665034)
06-07-2012 10:31 AM
Reply to: Message 292 by NoNukes
06-07-2012 12:53 AM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
Your example does not work because the method for inferring the design is presented as an assumption. By including a naked assumption that we can tell remotely whether a transit of a star is by an artificial planet, you simply kicked the can done the street. Do you have any idea how we would tell a designed transit from a natural one?
The paper describes a method whereby we could identify the shape of an orbiting body by its lightcurve signature. So, if we find that an orbiting body has an exotic shape (something not likely produced by gravity), we could reliably infer design - unless the author of this paper and many other scientists are wrong about inferring design.

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 Message 292 by NoNukes, posted 06-07-2012 12:53 AM NoNukes has replied

Replies to this message:
 Message 305 by NoNukes, posted 06-07-2012 1:32 PM Genomicus has replied

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


Message 299 of 337 (665037)
06-07-2012 11:09 AM
Reply to: Message 297 by jar
06-07-2012 10:39 AM


Re: Summary
We do not need the physical and specific lab. I already said that above.
Yes, and you also said:
"I assume that you have evidence of the lab?"
So, we need evidence of the lab, no?
You also said:
And "Yes, SETI will have to have the lab or at least the location of the lab that generated the signal."
So, yourself said that SETI would have to have the lab, or at least the location of the lab that generated this hypothetical signal.
Next, you said:
Of course you need to know how it was done.
And now you're saying we need a way how the signal could have been generated, and not how it was generated. There is a difference ya know. One has to do with possibility of how it was generated, the other has to do with the historical fact of how it actually was generated. So which one do we have to know to infer design? Specifically, why are you saying something that is contrary to what you said before?

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


Message 300 of 337 (665038)
06-07-2012 11:11 AM
Reply to: Message 248 by Coyote
06-06-2012 8:50 PM


Re: There is nothing to teach about ID...
Hello Coyote,
You will note that I do not at all agree with teaching ID in schools, precisely because it is not a rigorously developed hypothesis - not yet.
Further, ID doesn't imply that the supernatural even exists.

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


Message 302 of 337 (665040)
06-07-2012 11:23 AM
Reply to: Message 297 by jar
06-07-2012 10:39 AM


Re: Summary
That wasn't really explained and no evidence was presented that "front loaded genomes" exist, but it really doesn't much matter.
I've explained front-loading before, I've presented some clues in favor of front-loading, and you were present in the thread that I explained front-loading. Did you suddenly forget what front-loading is?
We do not see that when we look at examples of living critters. The humans brain is not then repeated in all mammals, the eagles eyes are not then repeated in all animals, good features, advances do not get incorporated across all the makes and models, species or kind, of mammals.
Have you ever tried putting the human brain in a shrew, jar?

Think about it.

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


Message 304 of 337 (665045)
06-07-2012 12:56 PM
Reply to: Message 303 by Panda
06-07-2012 12:49 PM


Re: Summary
Then what is preventing larger animals from having a human brain?
Human brains and the brains of larger animals (horses, etc.) are anatomically very similar. But anyways, it'd be pretty hard to front-load something as specific as a human brain.

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


Message 308 of 337 (665050)
06-07-2012 2:08 PM
Reply to: Message 305 by NoNukes
06-07-2012 1:32 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
I'm willing to believe that such a thing is possible in principle...
We're in agreement.

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


Message 310 of 337 (665052)
06-07-2012 2:13 PM
Reply to: Message 306 by NoNukes
06-07-2012 1:45 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
I think the answer is clearly NO.
Non-teleological evolution does not predict the deep homology of eukaryotic proteins with unnecessary but functional prokaryotic proteins, while front-loading necessarily predicts this. I can only reiterate what I said to Dr Adequate on why confirmation of a prediction of a model is superior to another model's explanation:
Consider the following example. Evolution predicts that if the bacterial flagellum evolved, a number of its components will share similarity with proteins that are more ancient than the bacterial flagellum. Can the hypothesis that the flagellum was engineered explain this? Yes. Engineers very often re-use parts in different systems. But the ID hypothesis does not predict that the flagellar components will share similarity with more ancient proteins. This is because engineers can also design from scratch. So, while ID can explain this, it does not predict it. Which means that, when it comes to similarity, evolution is the superior explanation (note that the similarity flagellar components share with other proteins is not incompatible with the hypothesis that it was engineered).
You say:
Further, I would dispute whether this is really a 'prediction' is a true prediction at all. It is not enough that the designer be teleological, or that the designer is using front loading. Instead the designer must have a particular front loading mindset that results in something that we already know to be the case.
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.

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


Message 311 of 337 (665053)
06-07-2012 2:15 PM
Reply to: Message 307 by Taq
06-07-2012 1:58 PM


Re: There is nothing to teach about ID other than as an example of pseudoscience.
You claim that all of these studies are able to detect design, yet they do not detect design where you claim it is. Perhaps you want to rethink your argument?
You're missing the point, Taq. I'm not looking for radio signals in the cell. But the principle of detecting design is the same among SETI scientists, and cryptographers.

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Replies to this message:
 Message 314 by Taq, posted 06-07-2012 2:22 PM Genomicus has replied

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


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. 34:175—184.
Pagel M. (1999) Inferring the historical patterns of biological evolution. Nature 401:877—884.

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


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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