Talk:Empirical ID research

From ResearchID.org

Wow, this page and news links are really cool. I found another prediction from an IDer (I think MikeGene) made, but I lost it in my reading. I'll try to find out where it is.--SierraEcho 14:43, 27 April 2006 (CDT)

Thank you for the compliment. :) A few more coming tomorrow...after I finish my last chemistry final. I have to say that MikeGene is one of my favorite ID authors, and that, at this point, my views and thinking are more similar to his than other IDists. Let me know what you dig up. -- JosephCCampana 14:51, 27 April 2006 (CDT)

You're lucky you have your finals now :-). I have mine in a couple weeks, but I've been swamped with problemsets. I put a bunch of stuff of stuff by MikeGene in my page just to keep them safe till we can decide where to incorporate the ideas.

(Btw, is it okay if we use 'IDer' instead of 'IDist'? It seems often labels that end in "ist" have a negative or partisan connotation.)--SierraEcho 15:14, 27 April 2006 (CDT)

1 Cees Dekker
- 1.1 Translation from FreeTranslation.com
- 1.2 Article about cod DNA
2 Proposed changes
- 2.1 Haldane Dillema

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Cees Dekker

Propose putting this somewhere here. Anyone know someone who could translate it?

Experimenten die ID kunnen aantonen (Article: Experiments that Could Demonstrate ID) --DLH 08:52, 7 July 2006 (CDT)

The following is a VERY rough translation of Dekker's article from FreeTranslation.com. This kind of gives you an idea where he is going, but is certainly not suitable to post at ResearchID.org in an article. Anyone know a person familiar with Dutch?

I happen to know a little bit of Dutch. I can try to clean up the translation over the weekend.--SierraEcho 20:04, 31 January 2007 (CST)

Hmm, it seems the original article has disappeared. Did you save a copy?SierraEcho 22:56, 8 February 2007 (CST)

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Translation from FreeTranslation.com

bionieuws 11, 03-06-2005

Experiments that could demonstrat ID

In an attempt a with respect to content discussion to lead over Intelligent Design has the editing at ID-sympathizer Cees Dekker asked experiments to consider that a design can demonstrate.

Through Professor. dr. Cees Dekker

professor Molecular Biofysica, TU Digs

Just shorten before: ID is not in my view a god-of-the-holes, someone else word for dit-weet-ik-nog-niet-dus-noem-ik-het-maar-ontwerp. ID is also not an at hoc creation through God that on discrete moments of the time just intervenes in the evolution. This is a wrong image is where you scientifically complete nothing with can.

ID is the idea that it a design to foundation lies at some structures in the nature and that this falls at to show on basis of scientific methods.1 Brand on that 'God' do not prevents in this definition.

On ground of the specific complexity of biological systems mean ID- scientists that the conclusion of an intelligent design in particular cases inescapably is.,. This complexity is visible in as well the modulaire structure as the information-content of living systems and trials. The first will one can compare with 'hard wired' technical systems, say an airplane, the second with an operating system as vastgelegd in a computer code. Living organisms had to interweave to be with information and information transfer. ID asks central attention for that information and the question how these generated becomes.

Complexity

Crucial for ID-investigation is the developing and apply of objective and trustworthy methods, with which you the existence of a design can verify, or falsificeren. How put you fast that something designed is? Within the biology only also the geology we see sometimes ultimately complicated patrons that explicablely are really through coincidence or laws of nature. Kepler meant for instance that the craters on the moon designed were, but we know now well better. How do we prevent such erroneous conclusion? With acumen from the information theory has mathematical William Dembski let see that an information-containing trial or object necessarily the qualities complexity and specificiteit knows.2 These qualities, vastgelegd in structure and semantic information-content, describe jointly the design of the system. Specificiteit points sees to that to a vastgelegd patron for the functionaliteit. Complexity points there to that the trial/object not simply predictably is and that one absolutely negligible chance (say smaller than 10-100) has through coincidence to arise. Such specific complexity cannot be declared through a law of nature or coincidences trials, and in our experience is an external intelligence the only causal source that we before know. The modern technique offers numerous examples by which 'intelligence' built in is (space shuttle, a computer chip). Dembski's complex specificiteit is a concrete criterion for the determining of design. After investigation concerned possible refinement of the method3 And application on concrete biological systems ID to test.

Concrete test objects find we in the celbiologie. Biochemicus Michael Behe has pointed on onherleidbaar complex systems that a set contain of superior, good in each other fitting and with each other variable work parts that each indispensable are for the original basis position.4 Remove of one of the parts has till consequence that the whole system no longer works.

Whip tail

The whip tail motors of a bacterium is the typical example. Through its onherleidbaar complex structure forms one problem for a direct darwiniaans scenario of advancing gradual evolution, because the all its components at the same time necessarily has for a position on which optimized can become by natural selection. After investigation is necessarily fixed to put or are concrete biomoleculaire systems herleidbaar complex, then well onherleidbaar complex. Until how far can systems be reduced to lose without their functionaliteit? Such investigation will have the character of reverse engineering of the structure and position of protein complex.

Biological ID-investigation concerned logical manner especially the evolution biology. A core question concerned the veranderbaarheid of a system. What evolutionair potential and which evolutionaire border knows a system? What is the creative, innovatieve power of the darwiniaanse principle of selection and accidental varition, and what be her borders? Are there also cases which the veranderbaarheid is ingeprogrammeerd in the biological system? What are the possibilities and limitations of evolution of a concrete protein system through mutation and selection?

Chance bill plays in this an important role. What is the chance that a new (part of a) protein arises? What do aminozuursequenties yield position? The answer can be been compared with the maximum number of possibilities in the available time. If the chance high is, furnishes the chance/selection mechanism a good explanation; as not, then not. First calculations let see that functional proteins sore infrequent prevent.5

This type investigation borders on already walking investigation on the territory of directed evolution and the novo protein design. ID stimulates was named designed the seeking to not-random mutations, preprogrammed variabiliteit and mutational derision as possibly long-term-survivals strategies. The possible position of 'junk-DNA' is also an example true ID a missing journey to position in the junk stimulates, while a darwinistisch perspective leads till the suggestion that one functieloos rudiment is. There are indications that junk-DNA indeed more position then has expected.6

Can we the principles of evolutionaire computers and ingeprogrammeerde variabiliteit use to generate complexity and how finds exchange place between complex specificiteit in the evolutionair algoritme to the realized end product? Can we something learn from the basis principles of technological evolution in industrial products which you as well evolutionaire development as revolutionary innovations see? Experience from industrial design can probably also methods pass that indicate in which extent a design optimally is, and such standards would can be applied on biochemische systems.

The origins of the life is an unsolved scientific question of large interest. Even the allersimpelste cells show an enormous complexity.7 How is such first cell ever arise? How quantify and objectify you the semantic information-content? What are the design principles in the architecture of the cell? What are innovations necessary by the realizing of a complex system? ID stimulates more to think from engineering drafts then from a samenraapsel that by coincidence with each other placed is. Where darwinistische scenarios more till organically growing complex networks lead, suggests ID a design of functional modules that with each other variable work. There are indications for such structure.8

Also interesting is investigation to the delineation of teleologie and autonomy in the nature. Biologists speak more than they self realize in teleological design question around position and target of molecular systems. An example of an ID-inspired result is the work of Denton eat already., that eiwitvouwing describe within a platonic idea of ideal forms.9 Also is the surprising high frequency of convergentie remarkable on many spots in the nature.10 How do we declare this? Ultimately is the interesting antropische coïncidenties in the biology11 after describing and crtically to consider: what is the play of parameters that biological life on earth permit?

People in the fur

Critics there in the right place on pointed that there till yet closed little specific ID-investigation was. Above have I what ideas for investigation indicated – partly already walking, partly with a new accent – where the idea of design fertile would be able to be. The time the learning will. A sceptical attitude with an open eye for new drafts appears me the healthy approach for such ID-investigation (and for science in the general). I expect that critics will complain that above list 'totally not newly' is. That is where and not where: not where because an ID-insteek well thoroughly someone else approach stimulates; only also well where because it in the practical execution science axis usual will be. Someone else putting into perspective is not plays that for 99 per cent of the biological investigation the question in the practice totally, or coincidence or design to foundation lies at the evolution. But the 1 per cent that is left is certainly interesting and of eminent interest.

An end remark: ID has crtically want to defy will become also a waardevolle as difficult people in the fur of the darwinisme, through the of evolutionaire claims and scenarios, through which – completely in style – the weaker way salary and the stronger in power will win. I think that darwinistische evolution on the long term more strongly built would be able to become by the challenges of ID, although probably with what bescheidener claims and a more accurate separation of science and metaphysics.

1. Dembski & Russian (2004) Debating Design, from Darwin to DNA; Dembski (2004) The Design Revolution

2. Dembski (2002) No Free Lunch

3. Ratzsch (2001) Nature, Design and Science

4. Behe of (1996) Darwin's black box

5. Axe, J. Molec. Biol. (2000); Axe, J. Molec. Biol (2004)

6. Johnston & Stormo, Science (2003); Makalowski, Science (2003)

7. Koonin, Nature Rev. Microbiol. (2003)

8. Alon, Science (2003)

9. Denton & mars hall, Nature (2001); Denton, mars hall & Lay, J. Theor. Biol. (2002)

10. Conway of Morris (2003) Life's solution.

11. Denton of (1998) Nature's Destiny.

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Article about cod DNA

Re the article about a section of junk DNA forming a gene for cod antifreeze, the significant point is that this is evidence for one process which evolutionists have accepted for many years.

Step 1: 'Junk' DNA is formed by mutations which prevent normal gene function. This can be by inactivation of a gene which was previously active. This is thought to be the way in which our ancestors lost the ability to synthesize vitamin C, but provided us with non-functional versions, pseudo-genes, derived from the vitamin C pathway.

Another source comes from gene duplication. Frequently having an extra copy of a gene has adverse consequences, so any mutation which inactivates, or reduces the activity, of one copy is favored.

Once a gene is no longer performing an important function, further random changes will accumulate in the DNA.

Step 2: One possible mutation is always the formation of a new 'Start' codon. Portion of the 'junk' DNA is then transcribed and translated into protein. The organism can then benefit, for instance, by having greater resistance to freezing.

An important result is that it becomes much harder to prove that a given change in DNA from that of species A to species B could not have occurred by mutation.

There is no need to find a sequence of single step mutations, each of which produces some increase in 'fitness'. One or more changes may have occured in a pseudo-gene which was not translated, and therefore had no adverse effects. After these changes occur by chance, the pseudo-gene can then be re-activated and be very advantageous.

--Keith C 13:54, 11 July 2006 (CDT)

Keith, thanks for the comment. I have not read the article you are referencing, so I thank you for your summary. I have a question regarding this feature:

"Random changes accumulate"..."One possible mutation is always the formation of a new 'Start' codon"..."occurred by mutation"..."these changes occur by chance."

With so many "random" and "chance" events needed to confer advantage, how "advantageous" is this mutation feature you're referring to? What is the name of this mutation feature you're referring to? Thanks, -- Joseph "Joey" C. Campana 14:26, 11 July 2006 (CDT)

Joseph,

The report which caused my comment was

http://www.radionetherlands.nl/features/science/060421rf

You or someone else provided this link on the 'Junk DNA' page.

The type of mutations I was considering was single nucleotide polymorphism, SNP.

If a gene has been duplicated, (and that does happen), and when this extra copy creates adverse effects, there are many possible SNPs which introduce 'stop' codons into the DNA.

Similarly, there are many different SNP's which will create 'Start' codons at some later time into the resulting pseudo-gene.

--Keith C 20:19, 11 July 2006 (CDT)

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Proposed changes

I suggest the comments on the Behe and Snoke paper should be changed to:-

In this article, Behe and Snoke attempt to calculate how difficult it is for unguided evolutionary processes to take existing protein structures and add novel proteins whose interface compatibility is such that they could combine functionally with the original proteins. Their hope was that by demonstrating inherent limitations to unguided evolutionary processes, this work would give indirect scientific support to intelligent design and bolsters Behe’s case for intelligent design via Irreducible Complexity in answer to some of his critics.

Unfortunately, this paper has itself been criticized.

Lynch, M., (2005) Simple evolutionary pathways to complex proteins , Protein Science (2005), Volume 14, Pages 2217-2225.

"It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size."

Behe and Snoke reply on pages 2226 and 2227 of same issue, [1]

Behe and Snoke do not answer Lynch adequately. Unfortunately, Lynch presents a different model and does not identify the specific errors made by Behe and Snoke. One point is that despite assuming a constant population size and neutral mutations, (other than the null mutations), Behe and Snoke replace any null mutation with a copy of the original duplicated gene with zero accumulated changes. (see paragraph 3. at bottom of first column on page 2654) A more consistent model would maintain organisms with one of the duplicate genes containing only one null mutation. Organisms which develop null mutations in both copies have to be replaced by multiplication of viable organisms, some with neutral mutations.

Perhaps you can find someone with a biological/mathematical background to provide a second opinion.

--Keith C 22:09, 12 July 2006 (CDT)

Keith C,

Thank you for your proposed changes.

Please discuss all article changes on the discussion page, not in the article itself.

As for your changes, this page uses extremely general information to summarize as much research as possible. It basically functions as a "gateway" page. Given this purpose: criticism, responses to critics, and criticisms of responses should be provided on a different page. If you would like to develop a criticism page, I invite you to do so. You will first need to develop the protein evolution article, and then develop your criticism under your user page at an article linked as something like User:Keith C/Criticism of Behe's protein research. (CC'd to Keith C's usertalk page) -- Joseph "Joey" C. Campana 07:38, 13 July 2006 (CDT)

Joseph,

Because the 'Protein evolution' page is to be a gateway, the text should not claim more than is clearly justified.

No, the Empirical ID research page is a gateway, the protein evolution page will be a research article with links to the full range of data related to the research.

Stating that "Behe and Snoke show how difficult it is for unguided evolutionary processes to take existing protein structures and add ....." is certainly not summarizing as much research as possible.

Summaries require equivocation. Actually, we need to make the summaries on this page shorter. Once we have linked research articles for all of the headings, we will be making the summaries on this page much shorter.

It is clearly stating only one position. I repeat my suggestion that you get a second opinion on the Behe and Snoke paper before you give it more emphasis than it deserves.

I have repeatedly asked many professionals to help us, but they are all too busy. If you know of any that have spare time to help us evaluate, I would be grateful for their input.

I suspect that a final year biology undergrad with a math background could give an opinion on Behe and Snoke and the Lynch papers in a couple of hours. A grad student would be even better. I have nobody in mind. I also do not know where you are located and what resources you have. Also, what procedure do you intend to use to resolve differences of opinion?

Grad students would be great! No one willing to "advise" our site, other than myself, has stepped forward thus far. Given this fact, I don't see how I, by myself can arbitrate the variety of contributions in all of our 85+ categories.

Therefore we intend to resolve differences of opinion the same way anyone else should: large doses of common sense, faithfulness to a mission statement, and having all (coherent and logical) views included or linked to. Please see our Research template, and note the criticism section.

As far as resources, to my knowledge there are no design proponents in any universities near me. Non-ID academics generally would not touch this website with a 300 foot pole for fear of the intellectual leprosy that would set in. -- Joseph "Joey" C. Campana 11:06, 14 July 2006 (CDT)

Perhaps the first paragraph in this section should be changed from

"This research gives indirect scientific support to intelligent design by demonstrating inherent limitations to unguided evolutionary processes."

to something more like:

"Most proteins function by catalysing specific chemical reactions. This page outlines information on the specificity of proteins and the problem of changing specificity by random mutation. Part comes from theoretical studies and part is evidence from experimental studies of actual proteins with mutations. Knowing any limitations to what can be accomplished by random mutation is important to identifying changes which require intelligent design.

This proposed paragraph would be supremely fit for the protein evolution article. If you would like to make the page, please feel free.

Then a sub-heading for Theoretical Studies

Then second heading on Experimental Studies

I'm assuming these "Then..." suggestions are for the protein evolution page?

Definitely all my suggestions from 12th and 13th are for the protein evolution page. Over next few days, I will have an attempt on part of that page. As you have discovered, my formatting will be a problem.

I'm glad you're going to start the protein evolution page, that's great! I look forward to reading it! I can help with formatting, no problem. Please see our Research template for how to start a new research article. -- Joseph "Joey" C. Campana 11:06, 14 July 2006 (CDT)

--Keith C 08:48, 13 July 2006 (CDT)

Keith C, thank you for your points of clarification. Please see my corresponding replies above, which are indented one tab in from your message. When replying on a talk page, please use colons to offset your comments from the those you are replying to. -- Joseph "Joey" C. Campana 12:08, 13 July 2006 (CDT)

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