Uncommon Descent Serving The Intelligent Design Community

Michael Yarus and the Thing that Couldn’t Die

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

MSTMichael Yarus, an emeritus professor at UColorado,  is one of the leading experts on the RNA World hypothesis, which takes the origin of life as flowing from RNA chemistry. His recent book with Harvard UP, Life from an RNA World, contains lots of material responding to ID, though without basic understanding, to say nothing of nuance.

The reason I bring the book up here, however, is to note his extensive use of Dawkins’ famous METHINKS IT IS LIKE A WEASEL evolutionary computing simulation. Yarus changes the target phrase to NOTHING IN BIOLOGY MAKES SENSE EXCEPT IN THE LIGHT OF EVOLUTION, but the essence of Dawkins’ simulation is nonetheless there in all its glory — indeed, Yarus develops this “instance of evolution” more extensively than Dawkins did. Moreover, Yarus sees this simulation as underwriting the power of evolutionary processes.

Dawkins’ simulation has come under considerable criticism both here at UD and at the Evolutionary Informatics Lab, where we have implemented “WEASEL WARE” (go here). Some internet critics have urged that we are beating a dead horse, that this example was never meant to be taken too seriously, and that if we were “serious scientists,” we would be directing our energies elsewhere. Let me suggest that these critics take up their concerns with Yarus.

The reason we keep bringing up Dawkins’ example is because evolutionists themselves won’t let it die. You can find Yarus’ discussion of it beginning on p. 64 of his book. It is available at Google Books here. Or you can view it below:

Comments
Off topic: This is the concluding statement of a talk by Alain Aspect on the overturning of Einstein's hidden variable argument: Part 5 - From Bell's Inequalities to Entangled Qubits: A New Quantum Age? http://www.youtube.com/watch?v=Pfg4M5okvxwbornagain77
June 12, 2010
June
06
Jun
12
12
2010
07:12 AM
7
07
12
AM
PDT
Dr. Dembski this radio broadcast may be of interest to you: Vaccines & Autism/Climategate http://www.coasttocoastam.com/show/2010/06/09bornagain77
June 12, 2010
June
06
Jun
12
12
2010
05:23 AM
5
05
23
AM
PDT
Just a brief comment about Yockey. While some of the things he says are interesting (and, I would say, very much ID), I was very surprised by this statement: Life originated, but must be taken as an axiom [something we know to be true, but cannot prove]. The problem in the origin of life that science is unable to solve is to explain how information began to govern chemical reactions through the means of a code. I oviously agree with the second part, but what about taking OOL as an axiom? I am always very surprised of how darwinist scientists, or even semi-darwinist scientists (if we can define Yokey that way), so often come out with such epistemological confusion. Darwinists are sadly famous for mixing up theories and facts, as thou thay were two interchangeable categories. And now, Yockey, a phycicist and information theorist, concludes that we have to treat OOL as an axiom. Now, just for clarity, I will paste here a very simple definition of "axiom" which, IMO, is good enough for our discussion: "A statement or formula that is stipulated to be true for the purpose of a chain of reasoning: the foundation of a formal deductive system". The problem is, axioms are a fundamental part of mathematics and logics. They are the basis of formal systems. Formal systems are deductive, and axioms are the only part of them which is accepted without any proof. That's because axioms are "stipulated". We have to remember that mathemathics and logics are the only sciences which are not empirical. They have no relationship with the existence of their "objects" as part of the outer world. The objects of mathematics are purely mental, and need not correspond to anything in the outer world. Therefore, when an axiom is "stipulated", it just means that the relative statement will be held as true in the formal system derived from it. Nothing less, nothing more. But empirical sciences do not work that way. Empirical sciences are interested in what exists in the outer worlds, and in explanations of what exists (finding regularities, building models, and so on). Empirical sciences do not admit "axioms". Empirical sciences start from facts, and build theories and models to explain facts. So, what is Yockey saying when he states that OOL cannot be solved, and must be takes as an axiom? As far as I can see, nothing which has meaning. That life originated is a fact, but that does not make it an axiom. How life originated is the correct question science has to answer. Now, while it is possible (but, I hope, not true) that that specific question will never be answered in a completely satisfying theory based on empirical data (indeed, we have no guarantee in principle that we will be necessarily succesful in explaining everything about reality), there is no possible reason to state that the question cannot find an answer in principle. So, defining it as an "axiom" is senseless, and it means to wrongly apply a concept of deductive abstract sciences to inductive empirical sciences. Empirical sciences allow no axioms. Thet vare only interested in facts, and in the explanation of facts. But I completely agree with Yockey that science is unable "to explain how information began to govern chemical reactions through the means of a code, if instead of "science" we specify "materialistic reductionist science whih refuses a priori to take into consideration consciousness and design as operating parts of reality". In that sense, Yockey's statement is perfectly true. But it simply points to a wrong scientific approach and prejudice, not to an objective impossibility. In the paradigm of design, OOL can and will be satisfactorily explained.gpuccio
June 12, 2010
June
06
Jun
12
12
2010
02:25 AM
2
02
25
AM
PDT
the lower limit of functional sequences is IMO completely bogus. It is based on a kind of approach which has deep methodological biases, both in the search method and in the definition of function.
The blog I cited indicated a very broad range of possible values. So research is just beginning. Silly me, having seen several hundred years of science find regularities in phenomena, I'm betting there are more regularities around the next corner. But I admit it's an unknown. We seem to have different expectations about what will be found. I will limit myself to one last slightly snide comment. It is easier to dig and not find a bone than it is to figure out how to increase the probability of finding a bone. It is easier to calculate immense improbabilities than to look for regularities that would reduce the improbability. The first approach simply assumes there are no biases in nature that would make the emergence and evolution of life possible. You calculate odds by assuming complex modern structures must come together all at once. The second approach assumes that there must be an incremental path. If I were to pick an ID proponent who makes sense to me it would be Michael Denton.Petrushka
June 11, 2010
June
06
Jun
11
11
2010
09:55 AM
9
09
55
AM
PDT
2)NS. In this kind of GA, the situation is completely different. The environment is completely passive, is not a programmed environment, does not recognize anything and does not promote anything. The selection takes plays because, in a situation of limited resources, the replicators compete one with the other. So, the function which is selected, not being recognized by any fitness function, must have in itself the power to confer a reproductive advantage. IOW, the function selects itself in the replicator, given the environmental resources
1. The "environment is not a single thing, physically or conceptually. The biological selecting environment includes the absolute necessities imposed by biochemistry. The replicator must have the structural elements necessary for metabolism and reproduction. The environment contains active predators and competitors. 2. To use Yockey's analysis, evolution cannot explain first life, but once life exists, replication, fecundity and pruning constitutes an algorithm capable of mining and digitally storing information about what works. 3. It is obvious from this analysis that the environment (in all the aspect listed above) must be permissive enough that some variations are not fatal, and that the mutation rate not overtake fecundity. So it is worthwhile to investigate the gaps argument and the entropy argument. The usual way to investigate such arguments is by research. They don't lend themselves well to axiomatic reasoning. Which is why I asked if anyone can name a species that went extinct through declining fertility associated with genetic entropy. An it's why I ask if there is any specific gap claimed in the last 150 years that has no been narrowed through research. Certainly research into blood clotting has yielded an array of incremental versions of blood clotting, not to mention alternative mechanisms. Pretty much the same is true of flagella and cilia. Many versions using various subcomponents and variations of components.Petrushka
June 11, 2010
June
06
Jun
11
11
2010
09:25 AM
9
09
25
AM
PDT
Walter Koover: In darwinian evolution, the environment provides the fitness function. As a semantic issue you may say that the environment does not choose, but from a conceptual point of view I don’t think it matters. It matters, It matters very much. And I definitely don't think I am mistaken. I am pointing to a very specific difference whic is often overlooked. Let's put it this way: 1) Men made GAs: they have a fiteness function which is designed by the programmer. The fitness function recognizes some properties, and, as you say, "determines which ones should be allowed to reproduce in greater numbers". The reproductive bonus is not a direct effect of the independent functionality of the replicator, but a bonus conferred by the system bevause of the recognition of a property which, in itself, would not give any reproductive advantage. So, the reproductive advantage is not spontaneouis, but "assigned" by an environment whose role is active, based on a logical recognition and an active procedure of "promotion". 2)NS. In this kind of GA, the situation is completely different. The environment is completely passive, is not a programmed environment, does not recognize anything and does not promote anything. The selection takes plays because, in a situation of limited resources, the replicators compete one with the other. So, the function which is selected, not being recognized by any fitness function, must have in itself the power to confer a reproductive advantage. IOW, the function selects itself in the replicator, given the environmental resources. This is a big difference, and poses a severe limit to what can be selected and what cannot.gpuccio
June 11, 2010
June
06
Jun
11
11
2010
04:54 AM
4
04
54
AM
PDT
OK... and this bears on the truth claims at issue how? Interesting reading, though. Meanwhile, let us not be distracted from you being under the obligation, as an intellectually honest guy (or gal) to show how the laws of physics can explain ANY code. Thanks in advance.tgpeeler
June 10, 2010
June
06
Jun
10
10
2010
07:58 PM
7
07
58
PM
PDT
gpuccio:
There are many equivocations about NS, as though something external is selecting, as though some fitness function is evaluating a result. That may be true for human made GAs, but it is not true of the model of darwinian evolution.
I think you are seriously mistaken here. In a GA the role of a fitness function is to discriminate among the "organisms" to determine which ones should be allowed to reproduce in greater numbers, isn't it? In darwinian evolution, the environment provides the fitness function. As a semantic issue you may say that the environment does not choose, but from a conceptual point of view I don't think it matters.Walter Kloover
June 10, 2010
June
06
Jun
10
10
2010
05:42 PM
5
05
42
PM
PDT
Interesting PDF regarding Yockey: http://www.idnet.com.au/files/pdf/Doubting%20Yockey.pdfPetrushka
June 10, 2010
June
06
Jun
10
10
2010
03:08 PM
3
03
08
PM
PDT
Yockey (2005) "The paradox is seldom mentioned that enzymes are required to define or generate the reaction network, and the network is required to synthesize the enzymes and their component amino acids. There is no trace in physics or chemistry of the control of chemical reactions by a sequence of any sort of a code between sequences."tgpeeler
June 10, 2010
June
06
Jun
10
10
2010
02:36 PM
2
02
36
PM
PDT
Petruska, since you will not be able to identify the origination of a single protein, nor the transformation of a existing protein, I will give you a easier task. Will you please tell me the natural source of the simple universal ATP energy molecule before the ATP synthase machine was "invented" since ATP molecules are required for the production of proteins. Evolution Vs ATP Synthase - Molecular Machine - video http://www.metacafe.com/watch/4012706 Molecular Machine - The ATP Synthase Enzyme - video http://www.metacafe.com/watch/4380205 This following video will give you a better Idea what I'm looking for: ATP Synthase - Part V http://www.dnatube.com/video/1201/ATP-Synthase--Part-V Now Petruska, I don't want a just so story of how a ATP molecule could have possible formed, I want you to tell me exactly how natural processes form the ATP molecule without the ATP synthase enzymnebornagain77
June 10, 2010
June
06
Jun
10
10
2010
01:31 PM
1
01
31
PM
PDT
I see now that anyway BA, with his usual efficiency, has already offered some reference about that. Thank you, BA. That pseudo value of functional sequences is one of the many myths built by darwinists for mere propaganda purposes, like the emergence of nylonase by frameshift mutation, the evolution of the flagellum form the T3SS, the "evolution" of the clotting system (even more ridiculous than the "evolution" of the eye), the various molecular "examples" of cooption (which I have discussed in some detail here with a biologist some time ago), and finally the emergence of the genetic code through supposed biochemical affinities of RNA and aminoacids. All these deserve at best to be treated as vague and very unreliable hypotheses, at worst as explicit lies.gpuccio
June 10, 2010
June
06
Jun
10
10
2010
01:27 PM
1
01
27
PM
PDT
Petrushka: the lower limit of functional sequences is IMO completely bogus. It is based on a kind of approach which has deep methodologocal biases, both in the search method and in the definition of fucntion. A se3rious analygsis of the paper which it is based upon would be very interesting, and maybe I will engage in that sooner orn later. But not now.gpuccio
June 10, 2010
June
06
Jun
10
10
2010
01:19 PM
1
01
19
PM
PDT
Petruska, this is the second or third time I've seen you appeal to Copernicus and Galileo, and the theory of Gravity. What you don't seem to realize is that both Copernicus and Galileo were devout Christians and were certainly not materialists as you are: "[It is my] loving duty to seek the truth in all things, in so far as God has granted that to human reason." Copernicus http://www.christianitytoday.com/ch/131christians/scholarsandscientists/copernicus.html Mathematics is the language with which God has written the universe. Galileo Galilei As well you seem to be under some delusion that gravity is explained to a material basis: REPORT OF THE DARK ENERGY TASK FORCE The abstract of the September 2006 Report of the Dark Energy Task Force says: “Dark energy appears to be the dominant component of the physical Universe, yet there is no persuasive theoretical explanation for its existence or magnitude. The acceleration of the Universe is, along with dark matter, the observed phenomenon that most directly demonstrates that our (materialistic) theories of fundamental particles and gravity are either incorrect or incomplete. Most experts believe that nothing short of a revolution in our understanding of fundamental physics will be required to achieve a full understanding of the cosmic acceleration. For these reasons, the nature of dark energy ranks among the very most compelling of all outstanding problems in physical science. These circumstances demand an ambitious observational program to determine the dark energy properties as well as possible.” http://jdem.gsfc.nasa.gov/docs/Decadal_Survey-Dark_Energy_Task_Force_report.pdf In fact, when scrutinized for details, the solution for the ultimate source for gravity (Dark Matter) lands squarely in the domain of Theism, so I would very much appreciate it if you would refrain to appealing to gravity to support your unsupportable conjectures for evolution.bornagain77
June 10, 2010
June
06
Jun
10
10
2010
12:00 PM
12
12
00
PM
PDT
Petruska please name just one biologically relevant protein to be IDentified with the 10^10 to 10^15 "forward approach" you mentioned: Szostak's 1 in 10^12 work for finding relevant functional proteins in sequence space has now been brought into severe question: A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells Excerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division." http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385 Having a randomly generated "protein" stick to the universal ATP molecule and then just calling it functional is a long step away from finding the correct sequence space for a protein that will actually accomplish a specific task as Axe's work does: Even though Axe's work puts the odd at 1 in 10^77 for finding a biologically relevant functional protein in sequence space, the odds are actually much much much worse against the evolutionists: Notes: Proteins have also been shown to have a "Cruise Control" mechanism, which works to "self-correct" the integrity of the protein structure from any random mutations imposed on them. Proteins with cruise control provide new perspective: "A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order." http://www.princeton.edu/main/news/archive/S22/60/95O56/ Cruise Control?,, The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent to me that highly advanced algorithmic information must reside in each individual amino acid used in a protein in order to achieve such control. This fact gives us clear evidence that far more functional information resides in proteins than meets the eye. For a sample of the equations that must be dealt with, to "engineer" even a simple process control loop like cruise control, for a single protein, please see this following site: PID controller A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. http://en.wikipedia.org/wiki/PID_controller It is in realizing the staggering level of engineering that must be dealt with to achieve "cruise control", for each individual protein, that it becomes apparent even Axe's 1 in 10^77 estimate for finding specific functional proteins within sequence space, may be far to generous, since the individual amino acids themselves are clearly embedded with highly advanced mathematical language in their structures, which adds an additional severe constraint, on top of the 1 in 10^77 constraint, on which of the precise sequences of amino acids in sequence space will perform a specific function. Though the authors of the paper tried to put a evolution friendly spin on the "cruise control" evidence, finding an advanced "Process Control Loop" at such a base molecular level, before natural selection even has a chance to select for any morphological novelty, is very much to be expected as a Intelligent Design/Genetic Entropy feature, and is in fact a very constraining thing to the amount of variation we can expect from a "kind" of animal in the first place. notes: Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe - Oct 2009 Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,, A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses. http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - May 2010 Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2 Testing Evolution in the Lab With Biologic Institute's Ann Gauger - audio http://www.idthefuture.com/2010/05/testing_evolution_in_the_lab_w.html “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed - along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) You can dream all you want petruska, but as I said before you have completely left the field of empirical science by refusing to concede materialism is bankrupt. In fact I have an extreme confidence that in the not to distant future the materialists of today will be seen as the flat-earthers of yesteryear.bornagain77
June 10, 2010
June
06
Jun
10
10
2010
11:36 AM
11
11
36
AM
PDT
Regarding Dougles Axe and the origin of proteins:
What is interesting is that the forward approach typically yields a “success rate” in the 10^-10 to 10^-15 range — one usually need screen between 10^10 -> 10^15 random sequences to identify a functional polymer. This is true even for mRNA display. These numbers are a direct measurement of the proportion of functional sequences in a population of random polymers, and are estimates of the same parameter — density of sequences of minimal function in sequence space — that Axe is after. 10^-10 -> 10^-63 (or thereabout): this is the range of estimates of the density of functional sequences in sequence space that can be found in the scientific literature. The caveats given in Section 2 notwithstanding, Axe’s work does not extend or narrow the range. To give the reader a sense of the higher end (10^-10) of this range, it helps to keep in mind that 1000 liters of a typical pond will likely contain some 10^12 bacterial cells of various sorts. If each cell gives rise to just one new protein-coding region or variant (by any of a number of processes) in the course of several thousands of generations, then the probability of occurrence of a function that occurs once in every 10^10 random sequences is going to be pretty nearly 1. In other words, 1 in 10^10 is a pretty large number when it comes to “probabilities” in the biosphere.
http://aghunt.wordpress.com/2008/12/26/axe-2004-and-the-evolution-of-enzyme-function/Petrushka
June 10, 2010
June
06
Jun
10
10
2010
10:35 AM
10
10
35
AM
PDT
P @ 79 "It seems odd to me that anyone would advocate abandoning a methodology that has worked so well for so long." Who's advocating that? Reason applied to evidence, that's the key. The problem with materialists is the rampant rejection of reason because reason always forces them to conclusions they detest. People are free to do whatever they will, of course (and answer for it) but it aggravates me to no end to labeled irrational by the irrational. Not that you are doing that in this snippet. I feel better now.tgpeeler
June 10, 2010
June
06
Jun
10
10
2010
10:35 AM
10
10
35
AM
PDT
Petrushka @ 78 Can you point to a law of physics, feel free to use all of them, that can explain a code, any code?tgpeeler
June 10, 2010
June
06
Jun
10
10
2010
10:31 AM
10
10
31
AM
PDT
Let me make clear my comment on destiny. A statistician looks at a lottery winner and assumes that given enough tickets and enough drawings, the odds favor someone winning. A biologist, looking at an unusual structure, such as the first eukaryotic cell, might wonder if this is an extraordinary event, or if it is as likely as someone eventually winning lotto. The answer to such questions can only be produced by research, some of it hard and perhaps taking generations. Science works by breaking hard problems down into pieces. Sometimes, when the pieces are understood, one can understand complex phenomena involving the pieces. It seems odd to me that anyone would advocate abandoning a methodology that has worked so well for so long.Petrushka
June 10, 2010
June
06
Jun
10
10
2010
09:27 AM
9
09
27
AM
PDT
It is interesting that you cannot even explain the origination of a single protein or even the transformation of a single protein for the flagellum...
Nor could Galileo or Copernicus explain gravity or define it mathematically. Sometimes hundreds of years go by before a phenomenon can be adequately described. Sometimes even useful mathematical laws are limited to a range of conditions. Can you point to a law of physics violated by insertions, deletions, frame shifts, inversions, missense, or duplication? Can you point to a law of physics violated by fecundity and differential reproductive success? Can you point to single complex structure in a living thing that does not have component parts used for similar or different purposes? Or a structure that doesn't have simpler versions in different organisms, or alternate versions having similar functionality? Can you describe the science behind a view of destiny that requires flagella to evolve? Did life not exist before flagella? Would it cease if flagella had not evolved? Did life not exist before eukaryotes? If they had not appeared, would life have ceased? I am curious why ID advocates look at what exists, whether the result of common and repeatable processes, or the result of rare or improbable events, and conclude that destiny requires it to exist. I am also curious why anyone would take seriously the argument that a pre-specified chain of mutations should occur, or that a chain that did occur should repeat itself.Petrushka
June 10, 2010
June
06
Jun
10
10
2010
09:01 AM
9
09
01
AM
PDT
It is interesting that you cannot even explain the origination of a single protein or even the transformation of a single protein for the flagellum, and yet you act as if pointing to something and "imagining" it transforming in your mind is somehow objective science: You are completely out of the realm of empirical science: Flagellum - Sean D. Pitman, M.D. http://www.detectingdesign.com/flagellum.html Biologist Howard Berg at Harvard calls the Bacterial Flagellum “the most efficient machine in the universe." Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_Abornagain77
June 10, 2010
June
06
Jun
10
10
2010
06:39 AM
6
06
39
AM
PDT
Petruska was the song in this video written "top down" from a mind or was it written "bottom up" by the machine? The Amazing Music Machine http://www.metacafe.com/watch/178495 Just as with this song or any other song is the flagellum and the blood clotting cascade, they must be implemented top down from a mind.bornagain77
June 10, 2010
June
06
Jun
10
10
2010
06:32 AM
6
06
32
AM
PDT
No one has effectively answered Michael Behe’s challenge on the blood clotting system in the form that he presented it.
Sounds like weasel words to me. Behe does not get to define reality. The simple fact is that the flagellum and the blood clotting systen are not irreducible in any way that has consequences for theories of evolution. Both have sub-components that appear in other organisms that lack the "complete structure." Both systems occur in orther organisms in simpler form. There are other implementations of the functions. All of these render the concept of irreducibility moot. There are no magic structures that cannot be slightly modified or which cannot exist in slightly different forms, or which do not use sub-components that are found performing different functions in other organisms. What you have is the equivalent of missing links -- a concept that erodes with time and research.Petrushka
June 10, 2010
June
06
Jun
10
10
2010
06:10 AM
6
06
10
AM
PDT
Here is a video on the flagellum that is fairly humbling to those who insist that it is "cobbled together" by Darwinian processes: Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 Steven Curtis Chapman - Dive (Concept Video) http://www.youtube.com/watch?v=F2v-wZP6I3cbornagain77
June 10, 2010
June
06
Jun
10
10
2010
04:21 AM
4
04
21
AM
PDT
Doug Axe has a article up at ENV: Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Suppose a secretive organization has a large network of computers, each secured with a unique 39-character password composed from the full 94-charater set of ASCII printable characters. Unless serious mistakes have been made, these passwords would be much uglier than any you or I normally use (and much more secure as a result). Try memorizing this: C0$lhJ#9Vu]Clejnv%nr&^n2]B!+9Z:n`JhY:21 Now, if someone were to tell you that these computers can be hacked by the thousands through a trial-and-error process of guessing passwords, you ought to doubt their claim instinctively. But you would need to do some math to become fully confident in your skepticism. Most importantly, you would want to know how many trials a successful hack is expected to require, on average. Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 1077 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 1077 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. http://www.evolutionnews.org/2010/06/doug_axe_knows_his_work_better035561.htmlbornagain77
June 10, 2010
June
06
Jun
10
10
2010
04:06 AM
4
04
06
AM
PDT
Petrushka: The blood clotting system is a formerly irreducible system that has many subsets among living organisms. And the E.coli flagellum is among dozens of flagella and cilia providing motility but having varying subsets genes and proteins. Not only is motility possible with subsets of genes, but there are quite a few varieties of such structures and quite a few different paths to them. First of all, the fact that a function can be implemented in different ways in different species, vith various sets of proteins, has nothing to do with irreducible complexity. We are well aware that different kinds of flagella and cilia exist. Behe just spoke about one type, and that has been enough, it seems, to give it eternal celebrity. But each single type of that machinery is, as far as I can understand, irreducibly complex. As is the ATP synthase, and probably all or almost all the compex biological machines, pathways and cascdes that we abundantly observe in all kind of cells (signaling form membrane to ythe nuclewus, apoptosis, the mytotic cycle, and so on). Regarding pathways, the clot issue is really very simple. Clotting has a common final pathway, with two alternative initiation pathways (intrinsic and extrinsic). Behe, probably for the sake of simplicity, analyzed in his book only the common final pathway. His argument in the book is about that. And, as far as I know, it has never been countered by anybody. About the flagellum, together with the many sources quoted by BA, you can also check, if you want, the "Frequently Raised But Weak Arguments Against Intelligent Design" section here, where we have tried to give our point of view, at point #33.gpuccio
June 10, 2010
June
06
Jun
10
10
2010
04:02 AM
4
04
02
AM
PDT
Here are a couple more references refuting on Blood clotting and the Flagellum: Miller's Failure To Refute Behe - Blood Clotting Cascade - Casey Luskin Excerpt: The lesson to be learned here is to always fact-check the claims of supremely confident defenders of Darwin like Dr. Ken Miller. He’s a very smart biologist. However, sometimes looking closely at his citations shows just how weak his arguments are. In this case, it seems very likely that Miller’s authority, Doolittle, had a very weak basis indeed for claiming that the lamprey lacked Factor V or Factor VIII. http://www.evolutionnews.org/2009/09/ken_millers_reliance_on_doolit025341.html The flagellum has steadfastly resisted all attempts to elucidate its plausible origination by Darwinian processes, much less has anyone ever actually evolved a flagellum from scratch in the laboratory; Genetic Entropy Refutation of Nick Matzke's TTSS (type III secretion system) to Flagellum Evolutionary Narrative: Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept... http://mbe.oxfordjournals.org/cgi/content/abstract/msn153v1 "One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later," Howard Ochman - Biochemist - New Scientist (Feb 16, 2008) Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video http://www.vimeo.com/9032112bornagain77
June 9, 2010
June
06
Jun
9
09
2010
08:04 PM
8
08
04
PM
PDT
Petrushka: Blood clotting and flagella. You are simply wrong on both points. No one has effectively answered Michael Behe's challenge on the blood clotting system in the form that he presented it. http://behe.uncommondescent.com/2009/01/miller-vs-luskin-part-1/ And the "paths" you speak about for flaggellar "precursors" are the biological equivalent of vapourware: http://behe.uncommondescent.com/2009/05/letter-to-trends-in-microbiology/SCheesman
June 9, 2010
June
06
Jun
9
09
2010
05:46 PM
5
05
46
PM
PDT
Isn’t the relationship between genotype and phenotype barely understood to this day? Aren’t “alleles” only really useful as a way to begin to teach undergraduates basic genetics?
I understand that at some time in the education of chemists they are told that everything the learned before is wrong. I'm not sure whether this impinges on the status of alchemy.Petrushka
June 9, 2010
June
06
Jun
9
09
2010
05:04 PM
5
05
04
PM
PDT
Nonsense. ID presents that as an observation and an inevitable result of chemistry and statistics. All you need to do to prove ID wrong is to fill in the blanks in a single case that has been presented as “irreduceably complex”.
The blood clotting system is a formerly irreducible system that has many subsets among living organisms. And the E.coli flagellum is among dozens of flagella and cilia providing motility but having varying subsets genes and proteins. Not only is motility possible with subsets of genes, but there are quite a few varieties of such structures and quite a few different paths to them.Petrushka
June 9, 2010
June
06
Jun
9
09
2010
04:51 PM
4
04
51
PM
PDT
1 2 3 4

Leave a Reply