Intelligent Design

[ricmat]

I’d like to see some of your friend’s ideas for his work that came from the TOE (and nowhere else).

Here is some published work on this:

mitre.org/news/events/exchange08/3046.pdf

defcon.org/images/defcon-14/dc-14-presentations/DC-14-Miller.pdf

1. These are not peer reviewed works.
2. These are software development design strategies.
3. The anti-malware software being developed looks at differences between known “bad” software to infer what a new “unknown” software executable might do. This is not new, it is not related to the TOE (although for buzz word impact, some might want it to appear as it does). There are no random mutations of the software which somehow enable the software to become more effective in detecting viruses.

Also…

A while back you (I think it was you ) asked for a definition of information. I provided one of the definitions given in Signature in the Cell. You didn’t respond.

Well, here’s another definition from M-W.com …

*2 a *(1) : knowledge obtained from investigation, study, or instruction (2) : intelligence, news (3) : facts, data b : the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects *c *(1) : a signal or character (as in a communication system or computer) representing data (2) : something (as a message, experimental data, or a picture) which justifies change in a construct (as a plan or theory) that represents physical or mental experience or another construct d : a quantitative measure of the content of information; specifically : a numerical quantity that measures the uncertainty in the outcome of an experiment to be performed.

2b is quite interesting

 

[M0nkey]

Actually the vast majority do nothing at all.

That is because it is a duplication, beings don’t typically mutate and when they do it’s bad news. BTW, I’m not following your logic.

Are you aware that cetecans lack parts of our blood clotting cascade, and yet their blood colts just fine. Are you aware that hagfish and lampreys lack even more of our blood clotting cascade and that their blood also clots just fine. There are many different ways to build a blood clotting system. We just have one possible version.

Are you aware that you are comparing apples and oranges? Let’s say for example I compare a biketoy to a motorbike and argue that it could have evolved by “numerous, incremental changes” however the truth is that the biketoy is a *conceptual *predecessor of a motorbike not a *physical *one. These systems all have very different designs, and to be clear all calculations shown have to do with vertebrate blood-clotting.

No. A single mutation could not have done so. A series of mutations could, and did, do so.

Duh, is that not what I implied? That a “series of mutations”, i.e., “evolved” into blood clotting? The fact is that you *believe *“mutations could, and did, do so” however the science says it’s near next to impossible. Random mutations do not add to our understanding other than *believing *that it just “happens.”

Going back to the cell, yes, it was implied which is why I corrected it to an animal cell. You have to watch the subtleties of what I write. This is a public forum, so I don’t have a lot of time to go into a lot of detail.

Your calculation is faulty. You have failed to include the element of natural selection in your model, so the numbers you are getting are useless. You probably also need to include the effects of sexual reproduction as well. Currently all you have is GIGO.

Why? Because it doesn’t square with your deeply held beliefs? Natural selection does nothing more than act on something that’s already there. The calculations were directly related to mutations, that is before natural selection can even take place.

 

[Just_Lurking]

1. These are not peer reviewed works.
2. These are software development design strategies.
3. The anti-malware software being developed looks at differences between known “bad” software to infer what a new “unknown” software executable might do. This is not new, it is not related to the TOE (although for buzz word impact, some might want it to appear as it does). There are no random mutations of the software which somehow enable the software to become more effective in detecting viruses.

You seem to be missing my point. What I am saying is that if the techniques used by evolutionary biologists are valid, then they will have applications far beyond the TOE. Similarly, if the techniques used by ID proponents are valid, then they will have applications far beyond trying to disprove TOE.

Well, guess what. Bioinformatics algorithms have widespread applications beyond evolution. Whereas all the blather from ID proponents has produced nothing useful. Just like the Young Earth Creations can’t find underground oil fields using their ideas.

A while back you (I think it was you ) asked for a definition of information. I provided one of the definitions given in Signature in the Cell. You didn’t respond.

That was tjm190 in post #36.

Well, here’s another definition from M-W.com …

2b is quite interesting

I want a mathematical formula that can be used to calculate the exact amount of information available in DNA. I’ve seen two different formulas used by ID proponents in a kind of “shell game” to hide the fact that the emperor has no clothes, but neither formula has the characteristics that ID folks claim, such as not increasing information content under random mutation.

If YEC’s really had a valid understanding of geological formation, they would be making billions of dollars finding new oil fields. But they don’t, so they aren’t.

If ID proponents really had a useful technique for detecting design, they would be making billions of dollars developing algorithms to automatically detect design that is being hidden by steganography and computer malware. But they don’t, so they aren’t.

If evolutionary biologists really had useful techniques for classifying traits and inferring inheritance, they would be using those techniques all over the place. And they are!

 

[M0nkey]

You seem to follow the logic that computer software is tantamount to the observable natural world. It does not.

 

[Just_Lurking]

I’m saying that the correctness of a scientific discipline can be seen by the useful results that it produces.

And that a methodology to detect and quantify design by intelligent beings that actually worked would have tremendous applications far beyond trying to prove or disprove TOE.

 

[rossum]

Are you aware that you are comparing apples and oranges?

I am not, as you will see.

These systems all have very different designs, and to be clear all calculations shown have to do with vertebrate blood-clotting.

Do you never think to look up words that you do not fully understand? Go away and look up the word “vertebrate”. Done that? Ok, now go away again and check whether or not cetecans (you can look up “cetecans” if you need to) are vertebrates. Now go and do the same check for “lamprey” and again for “hagfish”. Having done that can you work out why I used cetecans, hagfish and lampreys as examples in a discussion of the vertebrate blood clotting system? Yes, cetecans are vertebrates, hagfish are vertebrates and lampreys are vertebrates. There is more than one vertebrate blood clotting system. I merely gave some examples of different vertebrate blood clotting systems. By comparing the different vertebrate blood clotting systems we can see how they work and how they probably evolved. Vertebrate blood clotting systems are relevant in a discussion of vertebrate blood clotting systems don’t you think? In future please check first before posting - you are not doing your own side any good by posting this sort of stuff.

Duh, is that not what I implied? That a “series of mutations”, i.e., “evolved” into blood clotting? The fact is that you believe “mutations could, and did, do so” however the science says it’s near next to impossible.

You say that it is impossible, but I would suspect that you are not the most reliable scientific source available.

The calculations were directly related to mutations, that is before natural selection can even take place.

Natural selection has an effect on how many copies of a given mutation make it into the next generation. Later generations have their own mutations that will interact with the mutations present from earlier generations. Any calculation that leaves our the differential amplification effect of natural selection from generation to generation will come up with an incorrect answer.

rossum

 

[ricmat]

You seem to be missing my point. What I am saying is that if the techniques used by evolutionary biologists are valid, then they will have applications far beyond the TOE. Similarly, if the techniques used by ID proponents are valid, then they will have applications far beyond trying to disprove TOE.

But ID is not trying to disprove the TOE. To say such things diminishes your credibility. The vast majority of facts which support the TOE are accepted by ID as well. The only point of debate is with regard to totally “random”.

ID is very young compared with the TOE. Applications will come eventually.

Well, guess what. Bioinformatics algorithms have widespread applications beyond evolution. Whereas all the blather from ID proponents has produced nothing useful. Just like the Young Earth Creations can’t find underground oil fields using their ideas.

Ah, here we go again. Associate ID with YEC. Shame on you.

That was tjm190 in post #36.

Sorry…

I want a mathematical formula that can be used to calculate the exact amount of information available in DNA. I’ve seen two different formulas used by ID proponents in a kind of “shell game” to hide the fact that the emperor has no clothes, but neither formula has the characteristics that ID folks claim, such as not increasing information content under random mutation.

I don’t know what IDers have proposed in terms of formulas to calculate the exact amount of information in DNA. A large portion of Signature in the Cell involves information (Shannon, specified, complex specified, etc.) but I don’t recall a calculation (but it might be in there.)

But by analogy with computer programs, assume that an operating computer program (say, a few gigabytes long) has amount of information X. Random mutations can cause minimal, or severe, or crash disruptions depending on the details. One can say that if you get enough random mutations then it’s possible that something “better” happens. But when you start with a gigabyte long working program, your chance of fatal mutation induced garbage greatly exceeds any chance of a beneficial mutation.

And yes, I understand that in this analogy, you have billions and billions of computers simultaneously trying new randomly generated software. But even then…you do the math.

Random mutations to the works of Shakespeare, or software (which are much simpler than DNA) do not make for better works. There isn’t enough time, even if the random mutations worked at the theoretical fastest possible speed (limited by speed of light between participating molecules).

If evolutionary biologists really had useful techniques for classifying traits and inferring inheritance, they would be using those techniques all over the place. And they are!

Classification of traits is hardly unique to the TOE. Or inferring inheritance. If the TOE never came about, software would still be written, malware would be written, and people would make money writing anti-malware software. All of it designed. If random mutations are so great, then fire the programmers, and let the random program generator take over.

It looks like we’re not getting anywhere, but I want to get clarification from you on two questions.

1. Are you of the opinion that the development of complex life from e.g. single cell life was inevitable, or probable, or unlikely, or highly unlikely?
2. Are you of the opinion that the development of DNA from basic elements was inevitable, probable, unlikely, or highly unlikely?
3. Are you of the opionion that the development of the first “cell” from it’s constituent elements was inevitable, probable, unlikely, or highly unlikely?

Ok, so that’s 3 questions.

Also, if you can tell me exactly what is incorrect in Signature in the Cell (after reading it, and not before reading it), I’d appreciate it.

 

[buffalo]

No. Relative to what? No. No. No. Yes. Yes. Minimise energy.

How much chemistry do you know? Crystals are driven by chemistry and a bit of thermodynamics - the “Minimise energy” bit.

rossum

You seem to be stuck on crystals. My questions appear to anything that we are testing for design.

 

[Just_Lurking]

It looks like we’re not getting anywhere, but I want to get clarification from you on two questions.

I’m not sure we are getting anywhere either.

1. Are you of the opinion that the development of complex life from e.g. single cell life was inevitable, or probable, or unlikely, or highly unlikely?

Don’t know. Don’t care. I’m not a biologist.

1. Are you of the opinion that the development of DNA from basic elements was inevitable, probable, unlikely, or highly unlikely?

Don’t know. Don’t care. I’m not a biologist.

1. Are you of the opionion that the development of the first “cell” from it’s constituent elements was inevitable, probable, unlikely, or highly unlikely?

Don’t know. Don’t care. I’m not a biologist.

Also, if you can tell me exactly what is incorrect in Signature in the Cell (after reading it, and not before reading it), I’d appreciate it.

I don’t care about cells, so I won’t be reading it. I care about methods to detect and quantify the presence of design by intelligent beings. I just wanted to share my observation, made after studying several of William Dembski’s papers in depth, is that ID has contributed absolutely no useful ideas towards solving this problem. And that the people who do need to solve this problem, for real, as a part of their jobs and their paycheck, and who need to get the correct answer and not just B.S. around, make significant use of the ideas from evolutionary biology and bioinformatics, which actually do work.

 

[M0nkey]

I am not, as you will see.

Vertebrate blood-clotting systems are very different than any of it’s “predecessors.” The reason for mentioning that was to make it clear that this is what we are talking about notwithstanding your examples since you seem to have a penchant for not following a discussion. In short, the Irreducible Complexity of these vertebrates still stands. If you want to show it’s evolution you have to come up with a *physical *predecessor.

Natural selection has an effect on how many copies of a given mutation make it into the next generation. Later generations have their own mutations that will interact with the mutations present from earlier generations. Any calculation that leaves our the differential amplification effect of natural selection from generation to generation will come up with an incorrect answer.

Are you capable of following a logical argument? Natural selection has nothing to with “mutations.” It has to act on it as soon as a “workable” variation takes place, and I’ve shown you that it takes one hundred times more than the estimated age of the universe.

 

[M0nkey]

There is more than one vertebrate blood clotting system.

And seriously, stating the obvious won’t serve to win your case; it’ll only annoy people.

 

[rossum]

You seem to be stuck on crystals. My questions appear to anything that we are testing for design.

If the questions apply to anything then there are many possible answers, depending on the object being tested.

rossum

 

[hecd2]

Let’s deal with the basic question, could a “mutation” have evolved into a sophisticated system such as blood clotting?

OK - let’s deal with it. To begin with, no-one suggests that “a mutation” evolved into blood clotting. It is obvious that any complex pathway could not and did not evolve from “a mutation”. However complex pathways have been shown to be capable of evolving via multiple duplications and mutations over time via the co-option and modification of proteins for other functions and via the reorganisation of existing domains and motifs…

Remember, it takes a series of fine tuned cascades for it to work, think of machines working together. Not to mention the fact that any “mutation” in an organism is often catastrophic and the fact that by definition a *duplication *is only that a carbon copy of what was previously there.

The point about duplication is that it provides a second copy of a gene or set of genes. Since the original function is taken care of by the original gene, the copy is free to mutate to provide a new or different function. Analysis of many genes within a species show that they are organised in families of paralogues - different genes which all descend from a common ancestor via duplication and mutation. Important gene families of this kind include the HOX genes which are key to body patterning in development, many genes involved in host immunity and genes associated with sight and particularly with smell. Genes in the blood coagulation cascade are no different.

As for mutations being catastrophic - although catastrophic mutations do occur, many mutations have a small or zero effect on the organism, and ones that provide a benefit are more likely to fix in a population.

If you look at the numbers blood-clotting cascades have roughly 10,000 genes, each is divided into an average of three pieces giving you a total of 30,000.

This is gibberish. The blood coagulation cascade involves of the order of thirty genes not 10,000 genes, so your argument fails at step 1. As for “pieces” what do you mean by “pieces”?

TPA has four different kinds of domains.

By “TPA” I assume you mean tPA (tissue-type plasminogen activator). If you do, then what you write below is also gibberish in several different ways. The PLAT gene which codes for tPA has eight different transcripts formed by alternative splicing of the gene’s 14 exons. PLAT201, the protein that splices all exons, has five recognisable domains (a peptidase, two Kringle domains, an EGF-like domain and a fibronectin type 1 domain), but the “odds” you quote below are complete nonsense.

By “mutation” the odds of getting those four together is 30,000 to the fourth power, approximately one-tenth to the eighteenth power. Therefore, it would take an average of of a thousand billion years before *any *combination could work, which is roughly one hundred times more than our current estimated age of the universe.

This is nonsense in several ways:

1. No serious biologist would suggest that working tPA comes together in one step by the random shuffling of genomic fragments.
2. What is the 30,000? The probability “calculation”, would suggest that there are 30,000 utterly different things from which nature has to select the right four in the right order by throwing them randomly together. But just what are these 30,000 utterly different things?
3. There is no connection between the probability you present (which as we have seen is nonsense) and the average time to achieve it - it’s just a number that you appear to have plucked out of the air.
4. You completely ignore the fact that tPA belongs to a gene family and has 11 paralogues in humans. The following genes are in the same family in humans: HGFAC, F12, PLAU and HABP2, and all are assembled from the same domains.

In short, the calculation you present is worthless. (By the way, I do know that you have cribbed this almost word for word from “Darwin’s Black Box”, a discredited work by an utterly discredited author. It’s not *your *calculation after all - you don’t even understand it - but it’s still nonsense).

Alec
evolutionpages.com

 

[rossum]

Vertebrate blood-clotting systems are very different than any of it’s “predecessors.” The reason for mentioning that was to make it clear that this is what we are talking about notwithstanding your examples since you seem to have a penchant for not following a discussion. In short, the Irreducible Complexity of these vertebrates still stands. If you want to show it’s evolution you have to come up with a *physical *predecessor.

You seem not to be aware of the latest developments in Professor Behe’s study of IC systems. His own work, Behe and Snoke (2004), shows that an IC system can evolve. Are the various vertebrate blood clotting systems Irreducibly Complex - yes. Does this mean than they could not have evolved - no. Cetecans possess a large subset of the land-mammal blood clotting system which shows that that particular subset is functional on its own. Lampreys and hagfishes have a smaller subset which shows that those smaller subsets are also functional in the absence of the rest of the system. Our more complex system was built by adding more bits to an existing system.

If you want a physical predecessor, then how about Sea Squirts: The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes.

Are you capable of following a logical argument?

Yes.

Natural selection has nothing to with “mutations.” It has to act on it as soon as a “workable” variation takes place,

Natural selection has a great deal to do with what mutations survive from one generation to the next. Any calculation that covers more than one generation needs to include natural selection. Any calculation that assumes the de novo appearance of a complex system, such as blood clotting, in a single generation is nothing to do with evolution. Evolution is a process that takes place over generations; hence the need to include natural selection in the calculations. For an example of the sort of thing I am talking about see The Evolution of Boojumase

and I’ve shown you that it takes one hundred times more than the estimated age of the universe.

No you have not. You have stated it but you have not “shown” it. For instance, where did you get the figure of “roughly 10,000 genes” for the blood clotting cascade from? There are only about 30,000 genes to make an entire human being, I think it highly unlikely that one third of our genes would be devoted to this one subsystem. Your model only included point mutations and did not include gene duplications, indels, chromosome duplications or any other possible mutations. It did not include the effects of recombination and sexual reproduction. Your model did not allow for the evolution of the current system from a less complex predecessor, such as that possessed by hagfish.

Even within the 10,000 genes how many possible targets were there to aim for? There is more than one way to make a working protein for a given function. Obviously there are synonymous mutations, which your simplistic model made no allowance for, and then there are chemically similar alternatives such as replacing one hydrophilic amino acid with a different hydrophilic amino acid. Yockey (1992) calculated that there were 2.3 x 10^93 different amino acid sequences that would make a working Cytochrome C protein. The blood clotting proteins will have similar possibilities.

In short, your model was so faulty that the figures it produced were worthless. GIGO.

rossum

 

[buffalo]

If the questions apply to anything then there are many possible answers, depending on the object being tested.

rossum

Yup. :yup:

 

[buffalo]

http://www.kolbecenter.org/graphics/Jokemouse_sm.jpg

 

[ricmat]

I’m not sure we are getting anywhere either.

Don’t know. Don’t care. I’m not a biologist.

Don’t know. Don’t care. I’m not a biologist.

Don’t know. Don’t care. I’m not a biologist.

OK - you don’t care about biology because your’re not a biologist.

I don’t care about cells, so I won’t be reading it.

OK - you don’t care about cells because (I guess) you’re not a biologist.

I care about methods to detect and quantify the presence of design by intelligent beings.

Well, that’s awesome. Really. But isn’t it possible that the study of biological stuff, including cells, cross over into this area that you are interested in?

Meyer makes a good case IMO for design in the cell (and in DNA). You might get something out of the book even though you may end up disagreeing with the conclusions. You have only some time to lose by reading Meyer’s book. Or if you wish to save time and remain confirmed in your present ideas, you can just take somebody else’s word for it that there’s nothing there.

I just wanted to share my observation, made after studying several of William Dembski’s papers in depth, is that ID has contributed absolutely no useful ideas towards solving this problem. And that the people who do need to solve this problem, for real, as a part of their jobs and their paycheck, and who need to get the correct answer and not just B.S. around, make significant use of the ideas from evolutionary biology and bioinformatics, which actually do work.

If you’re not interested in biology, how do you come to know that their evolutionary ideas actually work? In fact, how do you know that these ideas are unique to, or originate in evolutionary biology? Perhaps they do, or don’t.

 

[MrZetterlund]

Nor does evolution since gills did not turn into lungs. Lungfish have both gills and lungs. Many amphibians have both gills and lungs. Gills develop from the Pharyngeal arches; lungs develop from the gut. They are different organs with different origins, lungs did not evolve from gills.

Were you there? Did you see it not happen? We already have fish with lungs - lungfish. A lungfish can survive for months away from water. Lungfish are related to Tiktaalik, a fish with gills, lungs and legs. Tiktaalik is related to Acanthostega, an amphibian with gills, lungs and legs. We are descended from Acanthostega or something very like it.

Your own personal disbelief is not relevant in science.

rossum

Did you know fish are the first animals created in Genesis?

 

[rossum]

Did you know fish are the first animals created in Genesis?

Did you know that we have fossils of animals like Kimberella which are not fish and appear in the fossil record long before anything remotely fish-like, with scales.

rossum

 

[Just_Lurking]

Well, that’s awesome. Really. But isn’t it possible that the study of biological stuff, including cells, cross over into this area that you are interested in?

There is a lot of cross over, which is why I have an awareness of the biological methods. But your questions related to evolution and biology proper, which I have no special expertise or interest in.

If you’re not interested in biology, how do you come to know that their evolutionary ideas actually work?

I’m connected with the computer science research community - my friend, the papers I linked to already, and so on. It turns out that computer viruses have a lot in common with biological viruses.

In fact, how do you know that these ideas are unique to, or originate in evolutionary biology? Perhaps they do, or don’t.

It’s irrelevant to me whether those ideas are unique to or originate in evolutionary biology. The point, at the risk of repeating myself until I am hoarse, is that the methods that they use in evolutionary biology (regardless of where those ideas came from) actually work. Whereas the methods that ID proponents tout either don’t really exist, or don’t really work to detect intelligent design in testable, real-world situations.