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  Topic: BIO-Complexity, the shiny new ID journal< Next Oldest | Next Newest >  
k.e..



Posts: 3840
Joined: May 2007

(Permalink) Posted: Aug. 31 2015,23:39   

Quote (Dr.GH @ Sep. 01 2015,06:30)
Quote (k.e.. @ Aug. 31 2015,17:11)
 
Quote (Leftfield @ Sep. 01 2015,02:53)
 
Quote (Henry J @ Aug. 31 2015,16:30)
Maybe notpologies?



Notractions?

Well as a vanity publication peer review free, it's mainly missing vanity.

And publication.
???

By definition one follows the other, either word is redundant.

--------------
"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
Bob O'H



Posts: 2175
Joined: Oct. 2005

(Permalink) Posted: Sep. 01 2015,03:36   

Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Clearly they're trying to rival the Journal of Universal Rejection.

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It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
OgreMkV



Posts: 3654
Joined: Oct. 2009

(Permalink) Posted: Sep. 01 2015,08:00   

Quote (Bob O'H @ Sep. 01 2015,03:36)
Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Clearly they're trying to rival the Journal of Universal Rejection.

Maybe it's just that their standards are so strident that their own people can't get...

Wait... no, that doesn't help them either. nevermind.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
KevinB



Posts: 340
Joined: April 2013

(Permalink) Posted: Sep. 01 2015,09:30   

Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

  
k.e..



Posts: 3840
Joined: May 2007

(Permalink) Posted: Sep. 01 2015,11:42   

Quote (KevinB @ Sep. 01 2015,17:30)
Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

Indeed why publish if the subject is obviously and indubitably self evident? There is undoubtedly a 100% surety that any superfluous tautologically redundant pleonasms that the ID crowd are fond of would just be sesquipedalian obscurantism. No wonder they don't publish they have nothing to say!

--------------
"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
NoName



Posts: 2721
Joined: Mar. 2013

(Permalink) Posted: Sep. 01 2015,12:21   

Quote (k.e.. @ Sep. 01 2015,12:42)
Quote (KevinB @ Sep. 01 2015,17:30)
Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

Indeed why publish if the subject is obviously and indubitably self evident? There is undoubtedly a 100% surety that any superfluous tautologically redundant pleonasms that the ID crowd are fond of would just be sesquipedalian obscurantism. No wonder they don't publish they have nothing to say!

And they say it at great, nigh unto interminable, length.

  
Henry J



Posts: 4689
Joined: Mar. 2005

(Permalink) Posted: Sep. 01 2015,14:13   

Yeah, isn't it funny how the ones with the least to say use the most words?

  
rthearle



Posts: 15
Joined: May 2005

(Permalink) Posted: Nov. 11 2015,17:25   

Just checked BIO-Complexity, the Discovery Institute's peer-reviewed journal, to see if they have published anything this year (they haven't, but it is only November). I did notice though that the last paper they published last year - Reeves/Gauger/Axe on enzymes - is listed with a citation of "BIO-Complexity 2014 (4):1−16". This struck me as rather odd since BIO-Complexity only published four papers last year in total.

A few moments of digging uncovered that BIO-Complexity is indeed publishing each article as a separate issue, even when they're just 6 pages long and published less than a week apart.

Is this normal for on-line journals? I haven't seen anything similar elsewhere. Or could it be an attempt to make their output seem greater than it is?

Roy

  
Henry J



Posts: 4689
Joined: Mar. 2005

(Permalink) Posted: Nov. 11 2015,20:26   

Re "Or could it be an attempt to make their output seem greater than it is?"

Surely not!

  
Bob O'H



Posts: 2175
Joined: Oct. 2005

(Permalink) Posted: Nov. 14 2015,05:57   

Online journals don't need to have issues, but the software they're using has that model. When a paper is published it's put online straight away rather than bundling it together with others as an issue. But the software is set up to publish papers in issues, rather than as they come, so this way they don't need to fight the system.

--------------
It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
REC



Posts: 638
Joined: Sep. 2006

(Permalink) Posted: Dec. 29 2015,18:04   

Wow....2nd 2015 publication from BioComplexity, and it is a doozy:

Axe and Gauger "tested these proposals by observing how the endpoint of simple evolutionary optimization depends on the starting point. Beginning with optimization of protein-like constructs in the Stylus computational model, we compared promiscuous and junk starting points, where design elements specific to the test function were completely absent, to a starting point that retained most elements of a good design (mutation having disrupted some). In all three cases, evolutionary optimization improved activities by a large factor."

Another round of  Axe and Gauger running experiments designed to fail, therefore design (except again, some worked, but you know, still design. Not evolution. Nope. Not ever).

Oopsy.

Much handwaving BS follows. Mostly that good 'designs' (defined by them as starting points closer to their target) perform better in a few rounds of directed evolution than more distant starting points, which they call promiscuous or junk (which are totes not-designed, cuz please they be evolutionary random 'junk'). Duh.

My favorite junky 'non-design' is a totally deranged protein* with a huge deletion which apparently fails to achieve full activity in a couple rounds of kit mutagenesis. This kit in my hands only changes a few bases per clone. No insertions more than a base. They don't try shuffling to mimic recombination. Shockingly, it didn't work!! But nearer starting points (again, called designs) do, therefore design and Jesus and all that.

*Their words: "In addition to the 36 residues that are missing in the deletion mutant, another 29 residues are unequivocally prevented from adopting the wild-type conformation because of the missing segment, meaning that the structural disruption extends to 65 residues. Because this is the minimum extent of impact to the whole structure, the images on the right show the maximum amount of wild-type structure that could remain in TEMΔ. What actually remains may be much less. In addition to the deletion, TEMΔ carries 32 amino acid substitutions (see Supplement S1 [28])"

When you read that, remember that TEM is ~280 amino acids.

eta: I'm actually most bothered by their misrepresentation of some very fine science.

eta 2: I wonder what the DI and UD say about this paper. Wonder if even they are a bit ashamed.

Edited by REC on Dec. 29 2015,22:55

  
stevestory



Posts: 10349
Joined: Oct. 2005

(Permalink) Posted: Dec. 30 2015,00:06   

Quote (REC @ Dec. 29 2015,19:04)
I wonder what the DI and UD say about this paper. Wonder if even they are a bit ashamed.

....uh...hmm.....um.....

   
rthearle



Posts: 15
Joined: May 2005

(Permalink) Posted: Dec. 30 2015,06:51   

From the Discovery Institute's latest peer-reviewed article comes a vital question:  
Quote
If we shared a digital versatile disc (DVD), is information being destroyed?
Answers on a postcard please.

  
sparc



Posts: 1970
Joined: April 2007

(Permalink) Posted: Sep. 11 2016,22:58   

Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Edited by sparc on Sep. 11 2016,22:58

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
timothya



Posts: 256
Joined: April 2013

(Permalink) Posted: Sep. 12 2016,05:48   

Quote (sparc @ Sep. 11 2016,22:58)
Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Since when does a user guide for a piece of software qualify as a scientific paper?

  
NoName



Posts: 2721
Joined: Mar. 2013

(Permalink) Posted: Sep. 12 2016,06:39   

Quote (timothya @ Sep. 12 2016,06:48)
Quote (sparc @ Sep. 11 2016,22:58)
Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Since when does a user guide for a piece of software qualify as a scientific paper?

Oh, don't ask that where Gary can hear you.
Next thing you know you'll be accused of bashing 'real-science'.

  
sparc



Posts: 1970
Joined: April 2007

(Permalink) Posted: Sep. 13 2016,03:40   

Since they already run a journal by he same name this could have been an opportunity for for the ID-creationists:  
Quote
11/22/2016
DARPA-BAA-16-08
Biological Technologies Office EZ BAA
BTO
This announcement seeks revolutionary research ideas for topics not being addressed by ongoing BTO programs or other published solicitations. Of particular interest are those proposals from entities (both small and large business) that have never received Government funding, or who do not normally propose to Government solicitations.
| Bio-complexity | Bio-systems | Health | Opportunities |


--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
sparc



Posts: 1970
Joined: April 2007

(Permalink) Posted: Nov. 08 2016,12:56   

Stop the presses: According to @DougAxe            
Quote
Ground-breaking computational model may sweep away the flimsy case for dismissing Adam and Eve. http://bio-complexity.org/ojs.........2016.3

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract:            
Quote
Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.
Looking forward for part 2.


ETA: They even discuss if the first couple could have lived in the Middle East.

Edited by sparc on Nov. 08 2016,13:46

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
sparc



Posts: 1970
Joined: April 2007

(Permalink) Posted: Nov. 08 2016,13:11   

Part 2 is actually appeared at the same time (http://bio-complexity.org/ojs.........2016.4).
I wonder why their model needs something that they call "created diversity" "for autosomal and X chromosomal DNA" "as a second source of variation"? Is there something special about the Y-chromosome?
Looking forward for the next paper which will explain how to dicipher the process of the formation of Eve from Adam's rib out of human genome data.

Edited by sparc on Nov. 08 2016,13:45

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
Henry J



Posts: 4689
Joined: Mar. 2005

(Permalink) Posted: Nov. 08 2016,13:11   

History Part 1? When Mel Brooks did a history part 1, he never got around to part 2, AFAIK. So it this about as intellectual as that was?

  
JohnW



Posts: 2816
Joined: Aug. 2006

(Permalink) Posted: Nov. 08 2016,18:06   

Quote (sparc @ Nov. 08 2016,10:56)
Stop the presses: According to @DougAxe            
Quote
Ground-breaking computational model may sweep away the flimsy case for dismissing Adam and Eve. http://bio-complexity.org/ojs.........2016.3

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract:            
Quote
Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.
Looking forward for part 2.


ETA: They even discuss if the first couple could have lived in the Middle East.

ID science at its finest.

1.  If Genesis was correct, we would expect to see DNA variation with certain statistical properties in the human population
2.  But in fact we see completely different statistical properties, incompatible with the account in Genesis.
3.  Add arbitrary Poof!
4.  Look again at the DNA variation.
5.  Repeat 3 and 4 until problem solved.
6.  Therefore Jesus.

--------------
Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"...  The correct answer would be "not even 0" - JoeG

  
Henry J



Posts: 4689
Joined: Mar. 2005

(Permalink) Posted: Nov. 09 2016,10:11   

Isn't "single couple" an oxymoron?

  
Acartia_Bogart



Posts: 1056
Joined: Sep. 2014

(Permalink) Posted: Nov. 09 2016,12:27   

These two papers has doubled the number of papers published this year. And two of the authors are on the editorial board.

  
Henry J



Posts: 4689
Joined: Mar. 2005

(Permalink) Posted: Nov. 09 2016,14:46   

Do they have any authors that aren't on board?

(That's if "on board" is the right term for those who missed the boat.)

  
sparc



Posts: 1970
Joined: April 2007

(Permalink) Posted: Dec. 10 2016,09:16   

Quote (JohnW @ Nov. 08 2016,18:06)
Quote (sparc @ Nov. 08 2016,10:56)
Stop the presses: According to @DougAxe              
Quote
Ground-breaking computational model may sweep away the flimsy case for dismissing Adam and Eve. http://bio-complexity.org/ojs.........2016.3

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract:              
Quote
Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.
Looking forward for part 2.


ETA: They even discuss if the first couple could have lived in the Middle East.

ID science at its finest.

1.  If Genesis was correct, we would expect to see DNA variation with certain statistical properties in the human population
2.  But in fact we see completely different statistical properties, incompatible with the account in Genesis.
3.  Add arbitrary Poof!
4.  Look again at the DNA variation.
5.  Repeat 3 and 4 until problem solved.
6.  Therefore Jesus.

Since Bio-Complexity's readership remains limited Gauger felt the need to further outline her breathtaking findings in an interview she gave to Salvo which actually lists Science only after Society and Sex in its header.
I am afraid though, that not even their sex pages are better than their science section.
(original link: http://salvomag.com/new........lap.php)

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
clamboy



Posts: 217
Joined: May 2006

(Permalink) Posted: Dec. 10 2016,12:16   

Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

  
Dr.GH



Posts: 2134
Joined: May 2002

(Permalink) Posted: Dec. 10 2016,12:46   

Quote (clamboy @ Dec. 10 2016,10:16)
Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

Did you see this little charmer, "Has Science Shown That We Evolved from Ape-like Creatures?" by Casey Luskin

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
clamboy



Posts: 217
Joined: May 2006

(Permalink) Posted: Dec. 10 2016,13:54   

Quote (Dr.GH @ Dec. 10 2016,12:46)
Quote (clamboy @ Dec. 10 2016,10:16)
Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

Did you see this little charmer, "Has Science Shown That We Evolved from Ape-like Creatures?" by Casey Luskin

Well, that was a waste of three minutes, thank you so bloody bloody much, Dr. GH. The entire site appears to consist of conclusions in search of any, ANY, justification.

The only benefit I've had in perusing their, um, "articles," has been the opening of my mental files in search of appropriate nouns: wingnuts...wackaloons...dingbats...spasmoids...im-BEH-ciles (a la Bugs Bunny)...cretins...dorkweasels...maroons (again, a la Bugs Bunny)...moronistic morons (a term my sister invented)...

  
Dr.GH



Posts: 2134
Joined: May 2002

(Permalink) Posted: Dec. 10 2016,21:25   

Quote (clamboy @ Dec. 10 2016,11:54)
The only benefit I've had in perusing their, um, "articles," has been the opening of my mental files in search of appropriate nouns: wingnuts...wackaloons...dingbats...spasmoids...im-BEH-ciles (a la Bugs Bunny)...cretins...dorkweasels...maroons (again, a la Bugs Bunny)...moronistic morons (a term my sister invented)...

:D  :D  :D  :D  :D  :D  :D

   
khan



Posts: 1528
Joined: May 2007

(Permalink) Posted: Dec. 11 2016,07:44   

Quote (clamboy @ Dec. 10 2016,13:16)
Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

One of the articles I read was anti-vaccine.

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"It's as if all those words, in their hurry to escape from the loony, have fallen over each other, forming scrambled heaps of meaninglessness." -damitall

That's so fucking stupid it merits a wing in the museum of stupid. -midwifetoad

Frequency is just the plural of wavelength...
-JoeG

  
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