Uncommon Descent Serving The Intelligent Design Community

A Simple Gene Origination Calculation

Categories
Intelligent Design
Share
Facebook
Twitter/X
LinkedIn
Flipboard
Print
Email

In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

Here’s the link to the abstract.

Comments
The burden of proof then obviously falls on the person who claims that languages can arise by means devoid of intelligence. Good luck with that.
In linguistics, a language is a set of strings (sentences) over a finite alphabet. Finite state machines, which should be familiar to DaveScot, are language recognizers. The type-3 languages of the Chomsky hierarchy of languages are precisely those recognizable by finite state machines. It takes only a two-state machine to recognize the language of all strings over {0, 1} of odd parity (containing an odd number of 1's). Does anyone REALLY want to argue that a physical system naturally modeled as a parity checker cannot arise by chance?CEC09
August 3, 2008
August
08
Aug
3
03
2008
09:50 AM
9
09
50
AM
PDT
One of the features of language is that they can be translated into other languages. For example, machine code can be translated into higer level code for us humans. German can be translated into French. Hofstader has written an excellent book regarding "information" and where it "is". By that I mean, what is the thing that is being translated, how can the essence be kept? He translates a single poem mutiple times into different languages and mutiple times (french into german into french again IIRC). http://en.wikipedia.org/wiki/Le_Ton_beau_de_Marot Can DNA also be translated in a similar way? If so, is anybody doing it? If not, does that indicate an interesting difference from "normal" languages such as English, German etc? Tribune7
If no, how does one determine whether unfamiliar objects are designed?
How do you determine that? What's your methodology? KairosFocus (from a post you link to above)
the speculations of OOL researchers are as a matter of fact as excerpted at above, poorly grounded relative to the chemistry and statistical thermodynamics involved
While I don't think there is much to get excited about in current OOL research I hold back from belittiling others efforts unless I have something concrete to add to the debate (and even then would hesitate to belittle others, treat others as you wish to be treated etc). Care to comment on what you think was the cause, rather then what was not?RitaFairclough
August 3, 2008
August
08
Aug
3
03
2008
09:40 AM
9
09
40
AM
PDT
DK It's actually an argument by analogy. Bfast accurately described the characteristics of several artificial languages then showed that the language of DNA conforms to those same characteristics. Unless you adhere to some unsupportable dogma that nothing in the universe predating humanity is artificial in nature then the best explanation for a language of unknown origin is that it is, like every other known language, artficial in origin. The burden of proof then obviously falls on the person who claims that languages can arise by means devoid of intelligence. Good luck with that.DaveScot
August 3, 2008
August
08
Aug
3
03
2008
08:30 AM
8
08
30
AM
PDT
Argument by definition. DK, you are using semantics to avoid the substance. Does design exist? Do designed objects have exclusive characteristics? If no, how does one determine whether unfamiliar objects are designed?tribune7
August 3, 2008
August
08
Aug
3
03
2008
06:30 AM
6
06
30
AM
PDT
bFast:
About Spiegelman’s monster’s determination to produce smaller and smaller RNA sequences that replicate. Now, Spiegelman published in ‘72. I am reading about Spiegelman in Wikipedia in 2008. My bet is that I am not the first to propose that the next logical question is “does the RNA ever increase in complexity?” My simple bet is that if subsequent experiments had produced RNA of increasing complexity, such would be published in Wikipedia under Spiegelman’s monster.
Note that Spiegelman was studying a reaction catalyzed by a bacteriophage (QBeta) RNA polymerase, using the viral RNA as template under highly specified in vitro conditions. Irrelevant to your expectations.
However, I am happy to be proved wrong. Please feel free to conjur up for me published evidence that simple RNA replicators will increase in complexity, and will begin to do anything more complex than just making copies of themselves (even making higher resolution copies would likely be useful.)
Sorry, don't know of any, but I'm curious: what do you mean by a "higher resolution copy"?Daniel King
August 3, 2008
August
08
Aug
3
03
2008
05:59 AM
5
05
59
AM
PDT
bFast #84:
One can therefore deduce that a reaonable definition of language is a syntax that communicates complex details between a sender and a recipient(s). By this definition English is a language. “C” is a language. and DNA is a language because it communicates complex details to the systems that assemble protein, to systems that replicate DNA, and to other systems not yet specified (control systems, etc.) It is a language, calling it a language is not “an analogy.”
Argument by definition. Completely convincing! Daniel King
August 3, 2008
August
08
Aug
3
03
2008
05:39 AM
5
05
39
AM
PDT
kairosfocus, I've read alot here from you in the last few days about what cannot have been the origin of life. I'd be more interested in what you think did happen. As best I can tell from your linked website, you consider the origin of life to have been a non-random event. Care to comment on what you think was the cause, rather then what was not?RitaFairclough
August 3, 2008
August
08
Aug
3
03
2008
03:27 AM
3
03
27
AM
PDT
I have usually given the words then the abbreviation in threads where I have used it.
Actually, a google search for "Functionally Specified Complex Information" site:uncommondescent.com links to 52 pages at UD. If the abbrevation FSCI doesn't appear in the same threads (which I doubt) this would result in about 170 comments (including KF's own) in which either the term or its abbrevation occurs. I did my best to look through the threads my original UD search linked to but I do admitd that due to the length of KF's comments which usually run over several screens it is difficult to identify comments by other users that used FSCI. You'll find comments on FSCI by Atom here, here, here, here, here, and here, comments by Phineas here, and here, comments by Carl Sachs here, and here, comments by aiguy here, and here, comments by Megan.Alavi here, and here, one comment by Frost122585 here, and one comment by JunkyardTornado here. You may add those that I've missed.sparc
August 3, 2008
August
08
Aug
3
03
2008
01:22 AM
1
01
22
AM
PDT
H'mm: Let me add this from TMLO, ch 8, as cited in my always linked Appendix 3:
Yockey7 and Wickens5 develop the same distinction, that "order" is a statistical concept referring to regularity such as could might characterize a series of digits in a number, or the ions of an inorganic crystal. On the other hand, "organization" refers to physical systems and the specific set of spatio-temporal and functional relationships among their parts. Yockey and Wickens note that informational macromolecules have a low degree of order but a high degree of specified complexity. In short, the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future. __________ Yockey: J. Theoret Biol, 1977, Vol 67, p. 383 Wickens: J. Theoret Biol, 1978, Vol 72, p. 191.
The links to my own descriptive term FSCI should be quite clear from the added emphases in context, and of course the CSI concept actually explicitly appears. Here is the 1973 Orgel remark:
Living organisms are distinguished by their specified complexity. Crystals fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.6 [Source: L.E. Orgel, 1973. The Origins of Life. New York: John Wiley, p. 189.]
The Specificity in view of course is bio-functional! GEM of TKIkairosfocus
August 3, 2008
August
08
Aug
3
03
2008
12:46 AM
12
12
46
AM
PDT
BFast: A quick note -- I have used the term Functionally Specified Complex Information, FSCI for short, to identify a subset of Complex, Specified Information that is specified as to function, with biofunction as a particularly relevant instance. [I have usually given the words then the abbreviation in threads where I have used it. BTW, there are at least a few other commenters here who have taken up the concept or the term. Cf here for a discussion of the underlying concepts and terms, including the perhaps surprising point for evolutionary materialists that the concept CSI emerged from the natural development of OOL studies at the turn of the 1980's -- contrary to a lot of ill-informed rhetoric out there, it is not a dubious innovation of ID thinkers such as Dr Dembski et al. Indeed, the first use of the concept I have seen is by ORGEL, in 1973.] Thus, we can get around several unproductive definitional debates and zero in on truly substantial matters. A closely related discussion is in Trevors and Abel, 2005, who look at Functional Sequence Complexity, vs Random SC and Ordered SC. (They have a very nice 3D graph, which I use in my app 3 the always linked.) BTW, Sparc, in 85, you have taken something utterly out of context when you cited two words only from 78:
[GEM, 78:] DK, I am simply citing Shapiro and Orgel. OOL studies is in utter disorder for those committed to evolutionary materialist models. But, we know a routinely encountered source of FSCI — intelligence. So, worldview agendas aside, why is this so often stoutly resisted as a viable alternative?
On basic grammar, "this" speaks to the just past where there is a chain of possible referents; in this case -- "intelligence." What is being "stoutly resisted" is not [a] the concept FSCI, but [b] the issue that the only -- and routinely -- observed source of functionally specific, complex information [and for that matter, after all the debates, CSI in general] is intelligence. And, there is abundant evidence of such stout resistance here at UD and elsewhere. Mind you, much of this is on side points and minor, potentially further distractive issues. I therefore observe that the evo mat side are still not seriously addressing the centrally important PaVian challenge at the head of this thread:
As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.” Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.
GEM of TKI PS to DK re 82: The basic fault with your argument about analogies is that you are failing to understand that D/RNA molecules are in fact discrete state informational macromolecules based on chains of 4-state elements and so having up to 4^N configs for a chain of length N, and involved in algorithmic information processing systems within the cell, tha tuse coded information. This is instantiation, not "analogy." BFast in 84 is quite right. (And I come at this as a "hardy boy" i.e. from the device physics and electronics side of the hard/soft distinction in modern electronics-based systems. "Digital" is not to be confined to electronics based, 2-state systems: our alphabet is a 26 state system, with extensions, and we commonly use 10, 12 and 60 state systems for working with numbers. The ASCII code is thus a 128 state system, which for electronics convenience codes in 2-state chained elements, where 2^7 = 128.) PPS, Sparc at 86 etc: Your citation of comments from former threads is quite besides the point (and I am sure that the search results are incorrect, off-point and misleading). As summarised above, I have simply used a subset of CSI where the requisite specification is provided by system functionality constraints. For instance, a random DNA strand has a basic chance of 3/64 that the next 3-letter codon will be a STOP codon. That is sufficiently high that random D/RNA chains are maximally unlikely to code a bio-functional protein. Such a protein has to have a folding sequence, and appropriate key-lock fit to its required environment, with appropriate functional units brought to bear, e.g. cf. the discussion of how enzymes are structured and work at 66 above. PPPS: DK at 81, the speculations of OOL researchers are as a matter of fact as excerpted at above, poorly grounded relative to the chemistry and statistical thermodynamics involved, in the case of the Miller-Urey type experiment propose an early earth atmosphere that is unlikely to have been there, and in the case of panspermia, the scenarios are utterly speculative. Quasi-infinite multiverse proposals are similarly a matter of speculation without observation.kairosfocus
August 3, 2008
August
08
Aug
3
03
2008
12:25 AM
12
12
25
AM
PDT
bfast
GEM of TKI, as you know I am another regular on this site, but somehow FSCI has slipped under my rader until now.
If you use the search link on the upper right corner of UD to look for FSCI you will find seven result pages (each with 10 results). Considering the 55 omitted search results FSCI has been mentioned about 120 times at UD only. Thus, it is not surprising that you have missed it.sparc
August 2, 2008
August
08
Aug
2
02
2008
10:35 PM
10
10
35
PM
PDT
GEM of TKI, as you know I am another regular on this site, but somehow FSCI has slipped under my rader until now. Could you clearly define the difference betwee CSI and FSCI. It would appear that CSI is information that specifies something complex where FSCI is information that specifies something that is both complex and functional. Is that about it? As I see it CSI includes some pretty non-functional concepts. For instance, the value of pi seems to be CSI. Certainly the value is complex. It specifies something -- the relationship between the radius and the circomference of a circle. As such it would qualify as CSI but not as FSCI, have I got this or am I barking up a different tree?bFast
August 2, 2008
August
08
Aug
2
02
2008
09:43 PM
9
09
43
PM
PDT
It won't change much but my FSCI numbers were wrong: I've missed 2 comments on KF's FSCI by Frost122585 and JunkyardTornado. So we now have a total of 16 opinions on FSCI at UD. Actually, I haven't looked for those entries omitted by the search engine because they are
very similar to the 55 already displayed.
sparc
August 2, 2008
August
08
Aug
2
02
2008
09:42 PM
9
09
42
PM
PDT
KF, FSCI (functionally specified, complex information) is not
stoutly resisted
here at UD but rather ignored. I am aware that FSCI is regularly mentioned by KF. However, only very few people here took the bait. According to the results of the UD search pages only 14 comments contain replies to FSCI statements (6 by Atom, 2 by Phineas, 2 by Carl Sachs, 2 by aiguy and 2 by Megan.Alavi) while FSCI to my best knowledge has never considered in the posts of Dr. Demski or any other UD contributor. I don’t know if this is the reason but as I understand FSCI it goes beyond Dembskian CSI and is defining some kind of The Edge of Intelligent Design by leaving the realm of ID as defined by the leading heads of the ID movement.sparc
August 2, 2008
August
08
Aug
2
02
2008
09:22 PM
9
09
22
PM
PDT
Daniel King, I follow your quote. If phenomenon X has a certain set of characteristics, and analogy Y also has the same set of characteristics, then analogy Y is a good analogy of phenomenon X. However, analogy Y may have some other characteristics which X does not have. Therefore when analysing the analogy rather than the phenomeon, one may be fooled into thinking that all components of analogy Y are part of phenomenon X. Now, DNA is a language -- it is not "like" a language. When we speak of the "machine language" of a computer's central processor, it is a language as DNA is a language, as english is a language. As a software developer I will often conjur up a new language to allow a user, or another software application to communicate complex material to my program. One can therefore deduce that a reaonable definition of language is a syntax that communicates complex details between a sender and a recipient(s). By this definition English is a language. "C" is a language. and DNA is a language because it communicates complex details to the systems that assemble protein, to systems that replicate DNA, and to other systems not yet specified (control systems, etc.) It is a language, calling it a language is not "an analogy." About Spiegelman's monster's determination to produce smaller and smaller RNA sequences that replicate. Now, Spiegelman published in '72. I am reading about Spiegelman in Wikipedia in 2008. My bet is that I am not the first to propose that the next logical question is "does the RNA ever increase in complexity?" My simple bet is that if subsequent experiments had produced RNA of increasing complexity, such would be published in Wikipedia under Spiegelman's monster. However, I am happy to be proved wrong. Please feel free to conjur up for me published evidence that simple RNA replicators will increase in complexity, and will begin to do anything more complex than just making copies of themselves (even making higher resolution copies would likely be useful.)bFast
August 2, 2008
August
08
Aug
2
02
2008
06:24 PM
6
06
24
PM
PDT
X has certain characteristics a, b, c Y has the characteristics a, b, c But Y also has other characteristics x, y, z. Therefore: X has the characteristics x, y, z. Daniel King, how is this bit of reasoning useful in the search for design? Because Hamlet does not have characteristic X while War and Peace does, are you saying that is an indication that one may not have been designed? Not all variables count, only the relevant ones.tribune7
August 2, 2008
August
08
Aug
2
02
2008
02:58 PM
2
02
58
PM
PDT
Paul Giem and kairosfocus, I trust that you will take the following in the helpful way that I intend it: Your arguments by means of analogy suffer from a logical problem that I learned about as a stripling. Neither of you would have passed my first year college course in logic if you had tried to defend such arguments. Here is a verbatim quote from my textbook, Monroe C Beardsley, Practical Logic, 1950, Prentice Hall, Inc., New York.
An analogy doesn't prove anything; it merely calls to mind a possibility that might not have been thought of without the analogy. It's the experiment that counts in the end. Bohr's classic model of the atom is only a picture. It has clarified some points about the atom, it has hinted at some good hypotheses; but if you take it as proving anything about the atom, you are misusing the analogy. You can be fooled just as much by it as were those early inventors who tried to construct airplanes that flapped their wings, on the analogy with birds. Analogies illustrate, and they lead to hypotheses, but thinking in terms of analogy becomes fallacious when the analogy is used as a reason for a principle. This fallacy is called the argument from analogy. The form of the argument from analogy is pretty clear from this simple example: X has certain characteristics a, b, c Y has the characteristics a, b, c But Y also has other characteristics x, y, z. Therefore: X has the characteristics x, y, z.
This from a professional logician, not a scientist. You are both entitled to your own opinions, but you are not entitled to your own logic.Daniel King
August 2, 2008
August
08
Aug
2
02
2008
02:46 PM
2
02
46
PM
PDT
Paul Giem,
It’s the naturalistic OOL researchers that engage in speculation against the evidence.
Hardly. Their speculations are grounded in chemistry and geology. The crux of the matter is that their speculations are subject to experimental test. Make a hypothesis and test it.
You denigrate the observation that DNA code is similar to computer code, calling it an analogy, and saying that it might lead to a hypothesis. I would argue that although by itself it may be weak evidence, it is in fact evidence, and thus to say that we are engaging in speculation without evidence is incorrect.
Not denigrate. An analogy is not an "observation" or "evidence." Again, make a hypothesis and test it.
But what may not always be appreciated is that we now have direct evidence for intelligence causing genetic change.
Intelligence, yes. Human intelligence.
Regarding the Spiegelman Monster, it seemed common knowledge enough to me not to have to document precisely where I got it. Obviously, you knew of it too. However, when I first ran into it, disappointment was expressed that the RNA didn’t keep getting bigger and bigger. I am still hunting for that specific reference...
The reference in question is: Kacian, DL, Mills, DR, Kramer, FR, Spiegelman, S Proc Natl Acad Sci USA 1972 Oct;69(10):3038-42. The abstract is clear enough:
The aim of the present study is to make available a replicating molecule of known sequence. Accordingly, we sought a molecule that has the following properties: (a) replicates in vitro in a manner similar to phage Qbeta RNA; (b) produces antiparallel complementary strands that can be separated from one another; and (c) is small enough to yield its sequence with reasonable effort.We report here the isolation of a replicating RNA molecule that contains 218 nucleotides and possesses the other features desired for a definitive analysis of the replicating mechanism. Despite its small size, this molecule can mutate to previously determined phenotypes. It will, therefore, permit the precise identification of the base changes required to mutate from one phenotype to another in the course of extracellular Darwinian selection experiments.
From the discussion of the paper:
Our goal was to isolate a molecule that replicates in a manner similar to phage Q? RNA and that was small enough to yield the sequences of its complementary strands. This goal has been achieved.
Do you read disappointment there?
Right now the evidence is against such a non-random pathway.
Evidence against. Please provide some.Daniel King
August 2, 2008
August
08
Aug
2
02
2008
11:11 AM
11
11
11
AM
PDT
PG: I see your somewhat concessionary excerpt/summary from DK:
You denigrate the observation that DNA code is similar to computer code, calling it an analogy, and saying that it might lead to a hypothesis.
This is not really "just an analogy." D/RNA is based on 4-state discrete state -- i.e. digital -- information storage elements used to implement stepwise control of a process. That -- like it or lump it -- makes it a digital, algorithm-linked information storage entity. So, properly: "instance of," not "analogous to." That the technology here is based on chemical monomers and shapes of molecules used is simply a matter of how the underlying digital entities are instantiated in a very much analogue physical world. (One of the biggest headaches of digital systems is that we have to implement them physically using very analogue entities . . . sigh!) Digital entities can be physically implemented in positions [cams, levers and gears -- cf a Yale lock], voltage or current levels, on/off states of relays and switches [my favourite first teaching system!], magnetic states, and in biosystems, as monomers in specified three-monomer codons in locations on smart polymer chains. In each case, chaining of discrete state entities allows for information storage and processing based on symbolic, coded representation and processing elements that respond to input and stored states. This is central, and decisive, once we see the resulting config spaces and constraints on functionality. Codes, step-by-step problem solving sequences that use codes and processing machinery and the like are not only routinely observed to be the product of intelligence, but that is the only observed source! A glance at the search space issues will show why: absent active information originating in intelligent insight and imagination, the search problem rapidly exhausts the potential search resources of the observed cosmos. GEM of TKIkairosfocus
August 2, 2008
August
08
Aug
2
02
2008
09:40 AM
9
09
40
AM
PDT
Daniel King, (69 and 75) It is easier to respond to your most recent posts, as they lay out the reasoning behind your belief. Part of an "honest diagnostic assertiont" is to give the limitations of evidence behind a diagnosis. As you noted, your expertise on naturalistic hypotheses on the origin of life is limited. And as kairosfocus noted (72), the experts of the two leading schools find it easier to state why the other guy's theory is no good than to make a good case for their own theory. The third most popular theory, that of clay first (the origin of Michael Ruse's attempted explanation of life originating on the backs of crystals in the movie Expelled) has nothing but speculation going for it. That is what the evidence says, as acknowledged by the leading researchers in the field. That's why it just blew me away when you said in (57) that we "assume that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation" and further stated that
Therefore, a scenario explaining life’s origins is not discoverable solely by speculation. What can be done empirically is to formulate hypotheses based on current understanding of the properties of matter (living and non-living) and its earthly history, and test them for fruitfulness in terms of increasing our understanding.
It's the naturalistic OOL researchers that engage in speculation against the evidence. You denigrate the observation that DNA code is similar to computer code, calling it an analogy, and saying that it might lead to a hypothesis. I would argue that although by itself it may be weak evidence, it is in fact evidence, and thus to say that we are engaging in speculation without evidence is incorrect. The evidence against other ways of getting life from non-life is also somewhat supportive of our position. But what may not always be appreciated is that we now have direct evidence for intelligence causing genetic change. DNA has been deliberately transferred from other flowers to roses, causing a change in their color. DNA has been added to bacteria and yeast by intelligent design; not just DNA for such things as insulin, human growth hormone, and tPA (tissue plasminogen acctivator), but for insulin that has been altered to change its degradation rate in humans. Thus we know that we can get DNA changes by intelligent design. Thus computer code has been proven to be a fruitful analogy and deserves to be taken more seriously than anti-ID websites commonly take it. In fact, this raises the question of whether "lateral transfer" should be reconsidered as a mechanism of DNA change. In fact, we have never (AFAIK) observed unassisted lateral transfer beyond about the level of bacteria. If we find bacterial rhodopsin in rice, we may be looking at assisted lateral transfer rather than unassisted lateral transfer. Regarding the Spiegelman Monster, it seemed common knowledge enough to me not to have to document precisely where I got it. Obviously, you knew of it too. However, when I first ran into it, disappointment was expressed that the RNA didn't keep getting bigger and bigger. I am still hunting for that specific reference, but may have found it in Robert Shapiro's book Origins. I will find out for sure by Monday. Even in the article I read cited by Wikipedia, the researchers stated that they hoped to be able to get longer strings of RNA so that subcellular (positive) evolution could be demonstrated, but I am unaware of any reports of success in that endeavor. You apparently agree with me that random formation of enough RNA to code for protein is extremely unlikely. The problem is that there is no known way to get sufficiently specific non-random sequences without intelligent guidance. That isn't to say that there will never be any known way in the future. But keep in mind that we are looking for "evidence", not "speculation". Right now the evidence is against such a non-random pathway.Paul Giem
August 2, 2008
August
08
Aug
2
02
2008
07:49 AM
7
07
49
AM
PDT
Magnan: Correct. Epigenetic information is also a key factor, and may actually encode even more information than DNA, through guiding how the embryo develops. This simply underscores the force of PaV's argument. GEM of TKI PS: DK, I am simply citing Shapiro and Orgel. OOL studies is in utter disorder for those committed to evolutionary materialist models. But, we know a routinely encountered source of FSCI -- intelligence. So, worldview agendas aside, why is this so often stoutly resisted as a viable alternative?kairosfocus
August 2, 2008
August
08
Aug
2
02
2008
01:40 AM
1
01
40
AM
PDT
Kairosfocus (#72): "....the projected mutation rate for Drosophila, a cluster of species that is part of the Diptera, and is notorious for its high variability, is vastly too low to account for the genome. In short, Darwinian mechanisms might account for micro-evolutionary changes, but not for the body-plan level changes that are the stuff of macroevolution." Yes, this is PaV's thesis in the original post, but the limited rate of origination of new genes understates the problem because the genes themselves only code for a fraction of the information to build organisms. To build newly modified organisms a lot more changes are required than new genes (however arrived at) and mutated old genes.magnan
August 1, 2008
August
08
Aug
1
01
2008
11:01 AM
11
11
01
AM
PDT
BTW in Biology it's "transcribed" not "transcripted". Not as bad as "transcripted proteins" that Jerry introduced at UD but still anoying.sparc
August 1, 2008
August
08
Aug
1
01
2008
08:32 AM
8
08
32
AM
PDT
kairosfocus, Thanks for the readings. I bow to your scholarship.
In short, neither of the major schools of thought rises above the level of highly speculative, empirically challenged models. A similar set of challenges apply to clay world, volcanic vent, cometary iceball, OOL elsewhere and transfer to earth by panspermia, and other proposed OOL models. “Speculative” is thus an apt, and perhaps even a charitable term to apply.
I agree. There are daunting challenges in that field. I'm happy to be merely an occasional student and spectator of those proceedings.Daniel King
August 1, 2008
August
08
Aug
1
01
2008
05:41 AM
5
05
41
AM
PDT
Frosty:
When we talk about design we are usually talking about issues of functionality- and DNA exhibits this in full. It is the form, function and improbability of the arrangement of matter that is needed be accounted for here. Intelligence is the only known cause of FSCI. Intelligence implies design—and, though weaker, a design(er).
Well put. GEM of TKIkairosfocus
August 1, 2008
August
08
Aug
1
01
2008
03:29 AM
3
03
29
AM
PDT
Yeah bfast, that would make sense. If simpler strands replicate faster, then that's all your gonna get. I think I remember Dembski going over this in NFL, glad to see wikipedia actually has an honest article about it. Must admit though, I think maybe they should come up with a different term then Spiegelman's "monster" if all it does is just lose complexity. I'll keep this in mind though for all origins of life discussions I get into from now on, seems like there isn't enough emphasis put on this.F2XL
August 1, 2008
August
08
Aug
1
01
2008
02:26 AM
2
02
26
AM
PDT
Re DK: Concerning: Speculative OOL models? First, though, onlookers, we should note that the PaVian calculation in the original post has yet to be seriously addressed on the merits by the evolutionary materialist advocates. The direct implication is that even on the generally accepted timeline, the projected mutation rate for Drosophila, a cluster of species that is part of the Diptera, and is notorious for its high variability, is vastly too low to account for the genome. In short, Darwinian mechanisms might account for micro-evolutionary changes, but not for the body-plan level changes that are the stuff of macroevolution. And, at the heart of that, lies the issue of information origination, another point where we seem to have a diversion from the issue on the merits. Getting back to the point raised by DK to PG, perhaps DK is not familiar with the recent exchange between Shapiro [a metabolism first OOL researcher] and the late Orgel [a RNA world OOL thinker], in which the fatal defects in the two main OOL models are painfully exposed: ++++++++++ SHAPIRO, Sci Am: The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life's building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case. A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate. To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . . The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck. _________ ORGEL, PLOS: If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . Could a nonenzymatic “metabolic cycle” have made such compounds available in sufficient purity to facilitate the appearance of a replicating informational polymer? It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield. Each proposed metabolic cycle, therefore, must be evaluated in terms of the efficiencies and specificities that would be required of its hypothetical catalysts in order for the cycle to persist. Then arguments based on experimental evidence or chemical plausibility can be used to assess the likelihood that a family of catalysts that is adequate for maintaining the cycle could have existed on the primitive Earth . . . . Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [6]? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . . The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help. +++++++++ In short, neither of the major schools of thought rises above the level of highly speculative, empirically challenged models. A similar set of challenges apply to clay world, volcanic vent, cometary iceball, OOL elsewhere and transfer to earth by panspermia, and other proposed OOL models. "Speculative" is thus an apt, and perhaps even a charitable term to apply. GEM of TKIkairosfocus
July 31, 2008
July
07
Jul
31
31
2008
11:39 PM
11
11
39
PM
PDT
sparc, "BTW, do other IDists share your opinion that random variation and selection both are intelligent processes?" sparc, you are putting words into gpuccio's mouth. You suggested that his claim that antibody generation is "engineered" is equivelant to saying that random variation is an intelligent process. This is a poor inference. If one can show that engineers use random processes than one can demonstrate that random processes are used by engineers. I would suggest that the random orbital sander is an excellent example of exactly that. As engineers clearly implement randomness as a component of their processes, when we see a "turn on random generator" phenomenon in nature, we can conclude that there is no inconsistency between nature and the metaphore of human-engineered technology.bFast
July 31, 2008
July
07
Jul
31
31
2008
08:26 PM
8
08
26
PM
PDT
gpuccio
an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen
The relevant sequences here are the v-genes of heavy and light chain loci. E.g., v-genes of the heavy chain locus are encoded by about 300 nt and you have about 200. As you said:
The 100 aminoacid protein is obviously a standard example, just to try a computation.
Even if one takes into account that CDRs are more relevant for antigen binding than FRs you're still left with a number nucleotides/amino acids that you assume to being beyond the edge of evolution. BTW, do other IDists share your opinion that random variation and selection both are intelligent processes?sparc
July 31, 2008
July
07
Jul
31
31
2008
11:58 AM
11
11
58
AM
PDT
Paul Giem: "Well, let’s see. Is the RNA world “speculation”, or a hypothesis with a lot of evidence behind it, and no major flaws created by the evidence? Or is it one of those “hypotheses” that should be “rejected”? How about the protein world? How about the clay hypothesis?" I have no idea. I don't work in those fields. (I wouldn't have the courage to attempt something so difficult.) What do those who are actually engaged in the research think? "Come to think of it, I seem to recall that DNA code is remarkably similar to computer code..." You have stated an analogy. Analogies might suggest hypotheses, and hypotheses might be tested. You have not made an argument. "That was insulting. But no more so than your comment that kairosfocus and I were assuming 'that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation.' " Insulting? No insult intended, and I am sorry if my honest diagnostic assertion came across that way. "There is a lot of experimental evidence to back us up." Is this a case in point? "RNA is supposed to polymerize with greater and greater complexity and function as time goes on according to the theory. Yet when RNA and the raw materials for RNA were put into a solution with RNA polymerase, the RNA sequences consistently shortened to the smallest fragments that would be reliably duplicated by the enzyme. That is, instead of evolution, we have devolution. This is actually understandable as survival of the fittest (who says the fittest has to be the biggest? If the only relevant function is reproduction, then smaller reproduces faster). But it doesn’t help the RNA to develop new functions, which it will need if it is to be a steppingstone to life." You did not reference the experiment, so I must guess at its provenance. It resembles something that came out of Sol Spiegelman's lab many years ago, the purpose of which was to examine the minimum nucleotide sequences required for replication of the RNA. The conditions in that work were set up to select for the "devolution" that was found. Do I have it right? If so, note the power of selection. Or this? "...so we need 20,000 bases. If we have all the nucleotides we want, a big if, and our minimum requirements are really the minimum and not woefully inadequate, another big if, we are looking at the random production of the long string of RNA that codes all this (with no stop codons and no signals as to where to start or where to cut the resulting RNA) having a probability of 1 in 4^20,000, or 1 in 10^16,666." This is a typical "tornado-in-a-junkyard" formulation. I have highlighted the word "random," because that is the crucial assumption that anchors this argument, and all such arguments. You are absolutely correct! Given the conditions you outlined, a random process is ludicrously improbable. But what scientist has proposed a scenario for RNA evolution based on random production of a 20,000 base RNA? "P.S. Some of us even think that there vas someone who vas dare, but then you don’t believe in old nomadic fairy tales, do you?" I suspected you thought as much. Thanks for the chuckle.Daniel King
July 31, 2008
July
07
Jul
31
31
2008
10:00 AM
10
10
00
AM
PDT
1 3 4 5 6 7 8

Leave a Reply