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Author Topic:   Can the creationist model explain the data?
Taq
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Posts: 6439
Joined: 03-06-2009
Member Rating: 4.3


(1)
Message 16 of 31 (808120)
05-08-2017 1:28 PM
Reply to: Message 13 by Faith
05-08-2017 1:25 PM


Faith writes:

I don't think you understand one thing about what creationists are trying to do.

We apparently know what the creationists are not doing, namely they are not producing a scientific model in the field of biology.

It would appear that creationists' efforts are more about theologic purity than about facts and science.


This message is a reply to:
 Message 13 by Faith, posted 05-08-2017 1:25 PM Faith has not yet responded

  
Taq
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Posts: 6439
Joined: 03-06-2009
Member Rating: 4.3


(1)
Message 17 of 31 (808121)
05-08-2017 1:29 PM
Reply to: Message 15 by Faith
05-08-2017 1:27 PM


Faith writes:

Do your victory dance. I'm out of here.

Thanks for proving our point.


This message is a reply to:
 Message 15 by Faith, posted 05-08-2017 1:27 PM Faith has not yet responded

  
herebedragons
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Posts: 1324
From: Michigan
Joined: 11-22-2009
Member Rating: 6.0


Message 18 of 31 (808122)
05-08-2017 1:30 PM
Reply to: Message 13 by Faith
05-08-2017 1:25 PM


I don't think you understand one thing about what creationists are trying to do.

Uhmm... trying to offer alternative explanations for biological facts that support their premise that evolution is wrong.

You find the approach foreign to your experience and if our different points of view are too different this isn't going to work.

So... not interested in real data. I see...

Thanks anyway.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 13 by Faith, posted 05-08-2017 1:25 PM Faith has not yet responded

  
herebedragons
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Posts: 1324
From: Michigan
Joined: 11-22-2009
Member Rating: 6.0


Message 19 of 31 (808125)
05-08-2017 1:36 PM
Reply to: Message 13 by Faith
05-08-2017 1:25 PM


What you are calling "analyses of data" comes from your own very different context HBD

You mean scientific training? Ok, sorry about that, I guess.

you are imposing conditions on creationists that are very likely irrelevant to what we are trying to do.

The question is: How do you explain the data? If you can't answer the question then fine, just do this:

Faith writes:

Forget it.

Do your victory dance. I'm out of here.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 13 by Faith, posted 05-08-2017 1:25 PM Faith has responded

Replies to this message:
 Message 20 by Faith, posted 05-08-2017 1:50 PM herebedragons has not yet responded
 Message 25 by Percy, posted 05-09-2017 8:36 AM herebedragons has responded

  
Faith
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Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 20 of 31 (808130)
05-08-2017 1:50 PM
Reply to: Message 19 by herebedragons
05-08-2017 1:36 PM


too bad because I would really like to see how this sort of discussion would go, but this is a set-up whether you mean it to be or not.
This message is a reply to:
 Message 19 by herebedragons, posted 05-08-2017 1:36 PM herebedragons has not yet responded

Replies to this message:
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Faith
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Posts: 24846
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 21 of 31 (808132)
05-08-2017 2:02 PM


Here's my laboratory experiment which I've mentioned before:

Collect a bunch of small creatures, small enough to let multiply in a lab but large enough to do DNA sampling on. Let them multiply, split them into new populations, let them multiply, keep doing this from each new population. Watch what happens to the genetic diversity.


Replies to this message:
 Message 23 by Taq, posted 05-08-2017 2:41 PM Faith has not yet responded
 Message 24 by RAZD, posted 05-08-2017 3:39 PM Faith has not yet responded
 Message 27 by Dr Adequate, posted 05-09-2017 12:18 PM Faith has not yet responded

    
Taq
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Posts: 6439
Joined: 03-06-2009
Member Rating: 4.3


Message 22 of 31 (808141)
05-08-2017 2:39 PM
Reply to: Message 20 by Faith
05-08-2017 1:50 PM


Faith writes:

too bad because I would really like to see how this sort of discussion would go, but this is a set-up whether you mean it to be or not.

How is it a setup?


This message is a reply to:
 Message 20 by Faith, posted 05-08-2017 1:50 PM Faith has not yet responded

  
Taq
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Posts: 6439
Joined: 03-06-2009
Member Rating: 4.3


(1)
Message 23 of 31 (808142)
05-08-2017 2:41 PM
Reply to: Message 21 by Faith
05-08-2017 2:02 PM


Faith writes:

Here's my laboratory experiment which I've mentioned before:

Collect a bunch of small creatures, small enough to let multiply in a lab but large enough to do DNA sampling on. Let them multiply, split them into new populations, let them multiply, keep doing this from each new population. Watch what happens to the genetic diversity.

The experiment for this thread is found in the opening post. Please address it.


This message is a reply to:
 Message 21 by Faith, posted 05-08-2017 2:02 PM Faith has not yet responded

  
RAZD
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Posts: 18462
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


Message 24 of 31 (808154)
05-08-2017 3:39 PM
Reply to: Message 21 by Faith
05-08-2017 2:02 PM


Here's my laboratory experiment which I've mentioned before:

Collect a bunch of small creatures, small enough to let multiply in a lab but large enough to do DNA sampling on. Let them multiply, split them into new populations, let them multiply, keep doing this from each new population. Watch what happens to the genetic diversity.

There have been several, mostly with fruit flies (short generations, DNA easily extracted).

See https://www.google.com/search?q=fruit+fly+experiments+dna...

Browse at your leisure, but there have been significant changes to their DNA over the period they have been done

Enjoy


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This message is a reply to:
 Message 21 by Faith, posted 05-08-2017 2:02 PM Faith has not yet responded

  
Percy
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Posts: 15622
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.4


(1)
Message 25 of 31 (808212)
05-09-2017 8:36 AM
Reply to: Message 19 by herebedragons
05-08-2017 1:36 PM


Looking at the data in Message 1, I have no tools (automated or otherwise) for its analysis. It would make no difference whether I was advocating the creationist or scientific position, I would be helpless. Perhaps it would be better if you presented your analysis, describing the patterns found and the implications. The rest of us can try to follow along.

I did try eyeballing the data and it seemed that species I is most distant from other species, and perhaps EFGH are more distant from ABCD, but I can't be sure.

--Percy


This message is a reply to:
 Message 19 by herebedragons, posted 05-08-2017 1:36 PM herebedragons has responded

Replies to this message:
 Message 26 by Taq, posted 05-09-2017 12:07 PM Percy has acknowledged this reply
 Message 28 by herebedragons, posted 05-09-2017 2:22 PM Percy has acknowledged this reply

    
Taq
Member
Posts: 6439
Joined: 03-06-2009
Member Rating: 4.3


Message 26 of 31 (808253)
05-09-2017 12:07 PM
Reply to: Message 25 by Percy
05-09-2017 8:36 AM


Percy writes:

Looking at the data in Message 1, I have no tools (automated or otherwise) for its analysis.

If you want to compare two of the protein sequences then you could use the Blastp alignment tool. You just copy and paste two of the protein sequences into the two boxes and hit the "BLAST" button towards the bottom. This is the result I got:

453 bits(1166) 1e-169 Compositional matrix adjust. 221/227(97%) 226/227(99%) 0/227(0%)

Query 1 MAYPFQLGFQDATSPIMEELSHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE 60
MAYPFQLGFQDATSPIMEEL HFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE
Sbjct 1 MAYPFQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE 60

Query 61 VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDS 120
VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDL+FDS
Sbjct 61 VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDS 120

Query 121 YMIPTQELKPGELRLLEVDNRVVLPMEVTIRVLISSEDVLHSWAVPSLGLKTDAIPGRLN 180
YMIPTQELKPGELRLLEVDNRVVLPME+TIR+LISSEDVLHSWAVPSLGLKTDAIPGRLN
Sbjct 121 YMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN 180

Query 181 QTTLMGTRPGLYYGRCSEICGSNHSFMPIVLELVPLSYFEKWSASML 227
QTTLMGTRPGLYYG+CSEICGSNHSFMPIVLELVPL+YFEKWSASML
Sbjct 181 QTTLMGTRPGLYYGQCSEICGSNHSFMPIVLELVPLTYFEKWSASML 227

The 221/227 (97%) is the identity score, meaning that 221 out of 227 amino acids matched.

If HBD were to include the sequences in FASTA format it would make it easier to dump these sequences in batch into other online tools. He may already have the text file in FASTA format.


This message is a reply to:
 Message 25 by Percy, posted 05-09-2017 8:36 AM Percy has acknowledged this reply

Replies to this message:
 Message 29 by herebedragons, posted 05-09-2017 2:57 PM Taq has responded

  
Dr Adequate
Member
Posts: 15928
Joined: 07-20-2006
Member Rating: 3.8


Message 27 of 31 (808255)
05-09-2017 12:18 PM
Reply to: Message 21 by Faith
05-08-2017 2:02 PM


Collect a bunch of small creatures, small enough to let multiply in a lab but large enough to do DNA sampling on. Let them multiply, split them into new populations, let them multiply, keep doing this from each new population. Watch what happens to the genetic diversity.

It increases. No surprise there.


This message is a reply to:
 Message 21 by Faith, posted 05-08-2017 2:02 PM Faith has not yet responded

  
herebedragons
Member
Posts: 1324
From: Michigan
Joined: 11-22-2009
Member Rating: 6.0


(1)
Message 28 of 31 (808272)
05-09-2017 2:22 PM
Reply to: Message 25 by Percy
05-09-2017 8:36 AM


General clarification of my preliminary point
Perhaps it would be better if you presented your analysis, describing the patterns found and the implications.

I plan to do that, but I wanted to make an important point before I presented my analysis. Perhaps I should take this opportunity to make my preliminary point(s) absolutely clear before moving on.

In order to analyze biological data there are 2 major requirements.

1) You must have an appropriate model.

Without a model you would have no context with which to even begin describing a set of data. CRR's point on another thread that biological problems can be solved with common sense and dredge's point that eliminating Darwinian evolution from biology would not make a bit of difference to understanding biological data are absolutely NOT appropriate models. Faith has the closest thing to a model, but if it can't be applied, it is not really useful. If these ARE appropriate models, they should be able to apply them to the data at hand.

2) You must have appropriate tools.

As you can see, even this simple data set is quite difficult to analyze and we are only dealing with 9 taxa and a protein that is only 227-aa in length. I even ordered the list of taxa so the pattern would be fairly obvious. Imagine a data set that consists of 30 taxa and a set of 5 genes that are each 700-800bp in length (~1250 amino acids after translation). The tools to analyze a data set like this were developed by evolutionary biologists based on an evolutionary model. The tools creationists use to analyze data seem to be limited to intuition and looking at things. Not too effective on real data.

The rest of us can try to follow along.

I will try to work through this step by step and will be adding taxa to further expand on not just how to do this type of analysis, but how evolutionary theory explains the patterns we see in genetic data. The hardest part will be getting things into a format that can be easily visualized on a website like this.

It would make no difference whether I was advocating the creationist or scientific position, I would be helpless.<...> I did try eyeballing the data and it seemed that species I is most distant from other species, and perhaps EFGH are more distant from ABCD, but I can't be sure.

Well... you have shown that you are not helpless in your approach this data. You apparently used a model that implies that organisms that are more similar genetically are more closely related. That is the most basic evolutionary principal and of course creationists can say that principal is consistent with their "model" as well. But as we expand this data set, the differences in models will become more and more apparent.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 25 by Percy, posted 05-09-2017 8:36 AM Percy has acknowledged this reply

  
herebedragons
Member
Posts: 1324
From: Michigan
Joined: 11-22-2009
Member Rating: 6.0


Message 29 of 31 (808277)
05-09-2017 2:57 PM
Reply to: Message 26 by Taq
05-09-2017 12:07 PM


Resources
I do have these in FASTA format. I presented it in interleaved format to make it easier to compare the taxa visually. I could also provide accession numbers, which would be easier than dealing with a whole FASTA file. If anyone is interested, let me know.

If anyone is interested in doing this for themselves, the software is available as free downloads.

For alignment and preliminary trees, I like to use Mega6. As I retrieved the url for the download, I saw they have a new version, Mega7, and I will upgrade to that soon.

For analyzing sequences and tree construction, I like PAUP4.0. Current build is 4.0a152. This is a time-expiring version, but it can be renewed after expiring.

I am hoping to use Mesquite for inferring ancestral character states. Current version is 3.20.

Data is available from NCBI database which includes a nucleotide database, protein database and BLAST tools (blast allows searching for similar or homologous sequences).

**Taq linked to the protein blast function at NCBI that allows comparisons.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 26 by Taq, posted 05-09-2017 12:07 PM Taq has responded

Replies to this message:
 Message 30 by Taq, posted 05-09-2017 3:46 PM herebedragons has responded

  
Taq
Member
Posts: 6439
Joined: 03-06-2009
Member Rating: 4.3


(2)
Message 30 of 31 (808285)
05-09-2017 3:46 PM
Reply to: Message 29 by herebedragons
05-09-2017 2:57 PM


Re: Resources
Here is the data in FASTA format:


>A
MAYPFQLGFQDATSPIMEELSHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLSFDSYMIPTQELKPGELRLLEVDNRVVLPMEVTIRVLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMGTRPGLYYGRCSEIC
GSNHSFMPIVLELVPLSYFEKWSASML

>B
MAYPFQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMGTRPGLYYGQCSEIC
GSNHSFMPIVLELVPLTYFEKWSASML

>C
MAYPLQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINSPSLTVKTM
GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMGTRPGLYYGQCSEIC
GSNHSFMPIVLELVPLAYFEKWSASML

>D
MAYPFQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLSFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMGTRPGLYYGQCSEIC
GSNHSFMPIVLELVPLVYFEKWSASML

>E
MAYPFQLGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTVRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMAMRPGLYYGQCSEIC
GSNHSFMPIVLEMVPLSYFETWSAVMV

>F
MAYPFQLGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMAMRPGLYYGQCSEIC
GSNHSFMPIVLEMVPLSYFETWSALMV

>G
MAYPFQLGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISSMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVILPMEMTVRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMAMRPGLYYGQCSEIC
GSNHSFMPIVLEMVPLSYFETWSALMV

>H
MAYPFQLGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETVWTILPAIILVLIALPSLRILYMMDEINNPSLTVKTM
GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTVRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMAMRPGLYYGQCSEIC
GSNHSFMPIVLEMVPLSYFETWSALMV

>I
MPYPMQLGFQDATSPIMEELMYFHDHTLMIVFLISSLVLYIIILMLTTKLTHTSTMDAQEVETIWTILPAVILILIALPSLRILYMMDEIYNPYLTVKAM
GHQWYWSYEFTDYENLMFDSYMIPTKDLSPGQLRLLEVDNRIVLPMELPIRMLISSEDVLHAWTMPSLGLKADAIPGRLNQITLTSSRPGVFYGQCSEIC
GSNHSFMPIVLEMASLKYFEKWSSMMQ

You can copy the entire section and then paste it into the window at Kalign if you don't like the idea of downloading random executables on the internet. Kalign has some simple phylogenetic analysis tools as well as simple comparisons between sequences. This is the % identity matrix for comparisons between all sequences:

#
#
# Percent Identity Matrix - created by Clustal2.1
#
#

1: A 100.00 97.36 96.48 97.80 93.39 94.27 92.95 93.39 83.26
2: B 97.36 100.00 98.68 99.12 95.15 96.04 94.71 95.15 84.14
3: C 96.48 98.68 100.00 98.24 94.27 95.15 93.83 94.27 83.70
4: D 97.80 99.12 98.24 100.00 94.71 95.59 94.27 94.71 84.14
5: E 93.39 95.15 94.27 94.71 100.00 98.68 98.24 98.68 82.82
6: F 94.27 96.04 95.15 95.59 98.68 100.00 98.68 99.12 83.26
7: G 92.95 94.71 93.83 94.27 98.24 98.68 100.00 98.68 81.94
8: H 93.39 95.15 94.27 94.71 98.68 99.12 98.68 100.00 82.38
9: I 83.26 84.14 83.70 84.14 82.82 83.26 81.94 82.38 100.00


This message is a reply to:
 Message 29 by herebedragons, posted 05-09-2017 2:57 PM herebedragons has responded

Replies to this message:
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