The Book is not the Ink and Hardware is not the Software

_{Barry Arrington

October 19, 2011

Intelligent Design}

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In this post the UD news desk quotes OOL researcher Jack Szostak: “We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited.”

He believes they have the “membrane” part figured out, which leads him to suggest that they are about “halfway” to figuring it all out.

Really? Consider a computer in a paper sack. If I figure out how to make a paper sack does that mean I am “halfway” toward figuring out how to make the computer-sack combo?

The other thing that caught my eye was in the comments. Joseph suggest that even if it is true that they are halfway there in figuring out the origin of the “hardware,” they have not even begun to figure out the origin of the “software” (which I take to mean the digital code in DNA).

To this, Dr. Liddle makes the astonishing reply: “The hardware is the software.”

No, Dr. Liddle. The medium is not the message. Your statement is akin to saying of a book, “The paper and ink are the novel.” This is obviously not so for the book. Why do you think it is so for the cell?

Comments

There isn't any evidence that the hardware is the software. The molecule is programmed- the program is the software.Joseph_{October 20, 2011
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Kelly:
How does ID explain the origin of the “information” you mention? If it’s not a property of the matter in which it is encoded then how *did* it get encoded into matter in the first place?
By design- just as programmers encode information onto a disc or into a prom
When/where/how/how many times etc?
That is what science is for. Geez your position doesn't have any answers and it has all the resources...Joseph_{October 20, 2011
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How about this java like snippet... Sequence mySequence = getSequence(DNA); Codon currentCodon = mySequence.getCodon(0); If (!firstCodon.equals(AUG)) { System.exit(-1); } Iterator it = mySequence.iterator(); while ( it.hasNext() ) { currentCodon = it.nextCodon(); process(currentCodon); }Eugene S_{October 20, 2011
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1.1.1.2 Elizabeth, Thanks. Question 1. Correct! Information exchange is successful only if you have a priori defined common: 1. alphabet. 2. language. 3. semantics. You are right, jibberish is defined only with respect to those three above, i.e. whenever something does not comply with the three above, it is jibberish. However, there may be defined common alphabet, language and semantics that what was jiberrish before, becomes a meaningful piece of information. There is no evidence of those three emerging at the same time with participants involved in information exchange. Information exchange rules may well become more elaborate on the go, but to kick off information exchange in the first place you need those three above well defined a priori. In practice this is defined by intelligent agents. There are no known cases of this being defined spontaneously. So by far the best explanation for information exchange if we see one is intelligent design. Question 2. While these may be of help, they are not critical for inferring design. Question 3. "It depends..." I define information in the sense of Shannon. Question 4. The answer is, "No known examples today". The difference is outlined here.Eugene S_{October 20, 2011
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kellyhomes: What's the problem with you? The sequence of nucleotides coding for a protein is obviously software. The nucleotides themselves, the physical gene itself, are obviously hardware. What's the problem?gpuccio_{October 20, 2011
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But the real problem is how do blind undirected purposeless forces accidently screw with chemcial toxic waste cocktails create even one intelligent code.
Well, yes, sort of, but lets remove the loaded terms however. Chemicals can only be "toxic" in the presence of something they are "toxic" to. So before you have something that can be poisoned, you don't have a poison. You might want to phrase that as "chemicals that are toxic to modern life forms". As for "waste" - again you viewing pre-biotic conditions from a post-biotic perspective - "waste", like "noise" and "weeds" is only meaningful relative to some thing someone wants. "Waste" is what is rejected by some process. Without some process to do the rejecting, you don't have "waste", and even when you do, it's a relative term! A wildebeest's "waste" is a dung beetle's dinner. And we've already got "undirected" in there, so we don't need "purposeless" or "accidentally", and "screw" is a bit emotive. Also "blind" and "undirected" essentially mean the same thing, so let's stick with "undirected": So let's edit: "But the real problem is how do undirected purposeless forces acting on a cocktail of organic molecules create even one intelligent code." And the hypothesis put forward by Szostak is that lipid vesicles, which form spontaneously within certain "cocktails" are permeable to organic monomers but not to polymers. As monomers enter the vesicle, those that form polymers are then trapped within it. Some of these polymers become self-replicators (we know of some self-replicating polymers but what these were is still up for grabs). The vesicles tend to grow, by "eating" other vesicles (this is the part the Szostak lab has been working on), so that they tend to grow into tubular structures that then tend to break up, simply owing to mechanical forces. If those vesicles contain self-replicating polymers, the "daughter" vesicles will "inherit" the sequence of polymer contained in the "parent". So we have the first information transfer - from "parent" to "daughter" vesicle. But so far the information isn't doing anything, so we might no even want to call it information. However, if certainly polymer sequences enhanced the chances that a vesicle would eat rather than be eaten, and divide successfully, clearly vesicles containing those polymers would start to dominate the vesicle population. And now we have evolution, and real information transfer, because the sequence of polymer actually contains "information", passed from parent to daughter, about how to enhance the chances of reproduction. It's not very intelligent code yet, but it's got something, and, more importantly, it's got something that can be built on.Elizabeth Liddle_{October 20, 2011
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Indeed, such language and degraded experessions are yet another part of your articles of faith and worldview as you see it.
Goodness me, Eocene! That's another allegation (slander IMO) that you need to support! And the standard of argumentation you seem to be rising to this morning is no higher than that of a playground! "well, you guys do it too, and anyway you smell". Since when did two wrongs make a right? And since when were "such language and degraded experessions" part of an atheist "articles of faith"? Atheists are people who don't find the evidence for God or gods convincing. Some think the evidence actually supports the position that they don't exist. Period. Now please stop tarring good people with a tarbrush of your own manufacture. Sure some atheists are rude. So are many theists. tbh you are being pretty rude right now!Elizabeth Liddle_{October 20, 2011
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kellyhomes: "And by not condemning but instead condoning Joe’s behavior those expressions are now part of your articles of faith too." ===== And what part of the "While I don't agree with the JoeG approach" didn't you actually get ??? Next time get a clue. On another note, the post you replied to him and refering to didn't actually have any of those JoeG-isms as you suggest. Rather you brought up the language issues which he and your side are prone to do on his own separate blog as even he readily admits, yet it had ZERO to do with any of the topic here or anything he actually said here. So apparently besides the "Burden Shift" tactics you are prone to use here, you also find "deflecting off topic" as another one of those adaptive traits when your answer Tank is running on empty. Maybe you should take off your own double standards glasses and view the real world.Eocene_{October 20, 2011
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1. Can you tell the difference between jibberish and a text that has a meaning, e.g. this post?
No. I can say for sure that a text is meaningful; I cannot say for sure that it is not meaningful.
2. When you see an ancient Egyptian or Chinese scroll can you tell that it was written by a human even though you may not know the language? To answer this question do you need to know how and on which medium it was written?
Yes, but I cannot tell whether it is jibberish or not. And while I would not need to know the medium in which it was written, I would need to know that it was written by in a medium that humans can use. That of course includes scrolls. I'd also need to know something about its provenance - how old is it? Were humans alive at the time it seems to have been made? Do we know that humans alive at that time had a written culture?
3. Do you agree that different parts of a biological cell pass information between them?
Depends how you are defining information. But in according to the Merriam Webster definition: "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", yes. The arrangement of nucleotides in DNA produce specific effects, for example the synthesis of specific proteins under specific conditions. Information could also be said to be passed from parent to progeny - information that produces the "specific effect" of causing the development of a phenotype with certain attributes, including attributes that will tend to enhance its chances of survival when compared with an ancestor in which those attributes were not present. This last kind of information - information regarding how to construct a phenotype well-adapted to its habitat - comes from the process of "natural selection" i.e. the differential reproduction of genotypic variants.
4. Can you give at least one provable example of genuine self-organisation (not to be confused with self-ordering)? Life does not count as such an example simply because we want to prove or disprove the ability of living systems to self-organise. So again, the question is whether you can give at least one example of self-organisation in the true sense in non-living matter.
Could you explain what you mean by self-organisation, and how it differs from what you call self-ordering? I asked you this on another thread, but can't remember where, so forgive me if you have already answered it.Elizabeth Liddle_{October 20, 2011
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Kellyhomes, Just some further ideas in addition to Question 2. To infer whether the script on the scroll has an intelligent cause, do you need to know who it was written by? In conversations like this one, do we always need to know the country of domicile, year of birth or the genuine full name of participants to conclude that they are humans, not malicious software?Eugene S_{October 20, 2011
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Kellyhomes, 1. Can you tell the difference between jibberish and a text that has a meaning, e.g. this post? 2. When you see an ancient Egyptian or Chinese scroll can you tell that it was written by a human even though you may not know the language? To answer this question do you need to know how and on which medium it was written? 3. Do you agree that different parts of a biological cell pass information between them? 4. Can you give at least one provable example of genuine self-organisation (not to be confused with self-ordering)? Life does not count as such an example simply because we want to prove or disprove the ability of living systems to self-organise. So again, the question is whether you can give at least one example of self-organisation in the true sense in non-living matter. Thanks.Eugene S_{October 20, 2011
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Yes, Craig Venter's , Gerald Joyce's and Nodel Laureate Jack Szostak's manipulating tinkering intelligences have all been well documented.Eocene_{October 20, 2011
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InVivo,
The plain existence of the cell as an exquisite assembly of hardware and software makes an even stronger argument that it was DESIGNED.
Here is a picture of a cell. http://www.mcb.ucdavis.edu/images/advising/cbi/cell-biology.jpg What is hardware? What is software? If you can't say, don't you need to reassess your "argument"?kellyhomes_{October 20, 2011
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KellyHomes: "Barry, How does ID explain the origin of the “information” you mention? If it’s not a property of the matter in which it is encoded then how *did* it get encoded into matter in the first place?" ===== Classic 'burden shift'! You can point to almost any OOL experiment done by an evolutionist to illustrate just how intelligence works and manipluates material componants. The problem is not how does intelligence create codes and encode material, we already know and relate to that in real life. But the real problem is how do blind undirected purposeless forces accidently screw with chemcial toxic waste cocktails create even one intelligent code. If the Miller/Urey experiments created intelligent codes as opposed to nothing more than rearranged material substrate, we wouldn't be having this conversation.Eocene_{October 20, 2011
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Indeed. It seems that many ID supporters have already made their mind up before they even know about ID and just see ID as validating those prior beliefs with "science" without looking much further into it then the surface claims (buy my book!). And when people move from the designer of life (which, after all, could be aliens) to "the world is designed" and "the cosmos is designed" then it's obvious that no alien could have designed the cosmos it itself lives in and that those people are really talking about god. A poor scientific facade indeed. It also illustrates the inability to actually rule things out of ID and why ID cannot ever be science in it's current form. For example, if the designer is what we understand as "material" it could not have designed the universe itself. That might have been a different designer. But ID cannot, will not, determine if there was more then one or a single designer. It cannot say if the designer is material or other. It cannot say if the designer acts constantly or just once or somewhere in between. What use is ID if it can't answer any questions at all? And if ID is about studying the design, Joseph, then what has ID discovered so far? Can ID tell me a single thing about anything that is currently unexplained? What is the origin of "biological information" Was it "designed"? Lol.kellyhomes_{October 20, 2011
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Kariosfocus,
Software is where EXPLICIT, prescriptive, functional info gets loaded into a digital system.
Could you give an example of where "software is loaded" in biology? As per comment 10. If software and hardware exist in biology then can you give a couple of examples of what specific biological structures represent hardware and software? Also how much ram does the hardware have? What programming language is the software in? One of the features of language is that it can be translated into other languages. Would you be able to translate some of the "biological software" into, say, Pascal? Or Forth? Or Python? If not, is "software" really the right name for it? Presuming that you can actually come up with some examples of "biological software" in the first place, of course.kellyhomes_{October 20, 2011
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Yes, it seems that designers are inclined to see design. Not surprising, perhaps.Elizabeth Liddle_{October 20, 2011
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Well, there are lots potential homologs with computers, but few are a perfect fit, and a cell is very different to a computer in many respects, no least being the fact that it self-replicates! One of the thing that bugs me a bit is the insistence on calling DNA "digital". It is only "digital" at the level of an entire population over time, in which some "digits" are shuffled and produce different phenotypes, which I think is a stretch. Much more interesting is switching at the level of the gene - discrete sequences of DNA can be switched on or off, depending on a cascade of on-off signals from elsewhere. But then we are not just talking about the cell being computer-like but the whole organism, and the "programming" of the cells happens during development, from the toti-potential early cells to the highly differentiated cells we end up with.Elizabeth Liddle_{October 20, 2011
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InVivo
As a person with a math and engineering education, I could not reach but a single firm conclusion: that our world is a DESIGNED world, that the LIVING WORLD is a DESIGNED world.
Funny how the vast majority of people who actually study *biology*, the field you are making claims against, disagree with you. Perhaps you should study some and then perhaps reassess?kellyhomes_{October 20, 2011
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We have full DNA sequences for many organisms now. Could you point to one such and show me where the "software" is encoded? Could you point to one such and show me where the "hardware" is encoded? If those two things do not make up 100% of the DNA for an organism how does ID explain the remainder?kellyhomes_{October 20, 2011
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Barry, How does ID explain the origin of the "information" you mention? If it's not a property of the matter in which it is encoded then how *did* it get encoded into matter in the first place? When/where/how/how many times etc? Can you tell me *anything* about that at all?kellyhomes_{October 20, 2011
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Eocene, I thought your side took the moral high ground? Instead we get X does it so it's OK if Joe does it too? Really? Previously Clive has banned people here for things they have said on other sites, unrelated to this one. I guess double standards are only OK if they help your supporters...
Indeed, such language and degraded experessions are yet another part of your articles of faith and worldview as you see it.
And by not condemning but instead condoning Joe's behavior those expressions are now part of your articles of faith too.kellyhomes_{October 20, 2011
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And yet that is what every intelligently directing manipulative mind of an Evolutionist has done when they rig an experiment for using a biased personal goal directed purposed outcome.
Please support this allegation.Elizabeth Liddle_{October 20, 2011
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And yet that is what every intelligently directing manipulative mind of an Evolutionist has done when they rig an experiment for using a biased personal goal directed purposed outcome. Gerald Joyce actually used previously and specifically intelligently designed replicating molecules working with a chemical catalyst in his experiment which out of necessity used a goal directing computer program to force and select the fittest molecules according to criteria of what Gerald Joyce's intelligent mind wanted/intended. The big problem comes later when Gerald Joyce later proceeded to fabricate a mythical RNA-World story of evolving molecules out competing other molecules for food, having offspring or babies, etc, etc, etc and all the while sneaking in the concept of self-awareness in this phony fabled RNA-World experiment. People just aren't that dumb anymore to believe in such myths, especially since lying and denying are neccesary to pimp this worldview of "No Intelligence Allowed".Eocene_{October 20, 2011
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I am a software engineer with tens of years of experience of implementing software systems.
I'm a hardware engineer, I frequently work with software engineers and unfortunately many of them, whilst being great coders, don't really get engineering.DrBot_{October 20, 2011
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I love the self-righteous indignation here. While I don't agree with the JoeG approach, your side uses such approaches X 10,000 if you were to ever visit any of the more popular Atheist combat forums where members are given a free hand at any manner of filth, vulgarities and insults. Indeed, such language and degraded experessions are yet another part of your articles of faith and worldview as you see it.Eocene_{October 20, 2011
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DrRec: "I hadn’t brought up religion. I don’t know Szostak’s beliefs. But apparently you are threatened by this research." ===== Yet the continued Faith statements of these experiments do point to a different type of religious worldview. Clearly faith, which is the belief in something not observed, but hoped for at a future time is exactly what this discussion is about. Nobody is arguing here against the actual processes involved in the carrying out of experiments. What they point out is that whether it's Craig Venter, Gerald Joyce(and his magic intelligently designed molecules) or a Nodel Laureate Jack Szostak, all of them using their collective intelligent minds formulate biased opinions, presuppositions, purposely intended goals of what they personally have reasoned with their own intelligence of just how life should have come about. Yet they clearly do meditate on the architectural plans and contemplative mechanical procedures of just how to construct just such nano-machine componants from materials they themselves have chosen and selected for. Doing so under environmental conditions their own religious predjudice has selected for and then further proceeding to pimp to what they consider a public who they consider complete imbeciles who need their superior guidance to understand anything. Then they take liberties in the explanation of their intelligently rigged experiment to fabricate a story line of a mythological prebiotic world where no intelligence existed and try and force feed this down others throats, all the while disconnecting their own intelligence from the explanation. Yet they(Evolutionists) apparently need constant reminding of their own religious FAITH = "NO INTELLIGENCE ALLOWED". Even hardware has instructions for it's manufacture, but it's those instructions that comes first and this is all they have ever proven when they continually manipulate, rig and guide every experiment with their own goal driven intelligent minds. It's the lying part in discounting or disconnecting their own intelligence as having nothing to do with these experiments that others don't like. Most people are not simple minded ignoramuses. Try as you might to distance yourself from faith and required intelligence is an impossible goal here. You continually prove what you aim to refute. Clearly you are wanting others not of your FAITH to believe in your own chosen FAITH(No Intelligence Allowed) and that just isn't going to happen very easily when you support the hijacking of I.D. concepts in experimentation and then proceed to lable it blind undirected forces and deny it's anything of the sort. This isn't about the Great Shamman storytelling time around a Kampfire and most modern people today aren't ignorant guillible tribesman who will in fear obediently hang on your every word as some supposed mystic truth. ----- DrRec: "I understand your reaction better now. I also don’t think anything I say, or the progress of the field will impress you much." ===== Yes, ultimately I'd say it safe to say your continued prosyletizing probably won't move others to apostacize from their own previously held religious beliefs and convert to your brand of faith based beliefs espoused by your Church. The main difference here between the two sides is that the I.D. crowd will admit they have an element of faith they work with. Your side by necessity latches onto faith and allows it to influence everything they do and say and then turns completely right around and denies it is anything of the sort at the same time. It's almost like your side in it's attempt at research is in effect employing the old joke line: "Look Up. Look down. Look all around. See my thumb, gee your dumb."Eocene_{October 19, 2011
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"The sequence of protein or RNA produced by DNA is a direct consequence of the order of the chemical bases on the DNA." Yes, but the sequence of the DNA bases is not determined by the property of the matter (i.e., the nucleotides). Information is not the same as the medium in which it is encoded.Eric Anderson_{October 19, 2011
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DrREC, I didn’t brought up religion explicitly myself – but to sympathize with Bornagain77's opinion. I am not shy though to bring it in our discussion. Let me help you with explaining my thinking. I am fascinated by science. Although a software engineer, I started paying attention for the last 10 years to biology, molecular biology, genetics, origin of life, etc. I keep an open eye to the research and current understanding of particles physics, astronomy and astrophysics, cosmology, history, geology. I think that being a software engineer gave me some understanding how working systems can be designed, assembled, constructed. That gave me also a basis to evaluate and compare the complexity and intricacy of some sorts of human artifacts (computers, computer-based systems) and the living world creatures – that I sometimes, through a crude and unfair simplification – tend to see as machines. I am very interested in the Origin of Life research and I did some reading in this area. I am following the news in this domain. I have some “preconceived ideas” related to this research. But those ideas were though “conceived” and structured after educating myself in systems theory, a little in the molecular biology, the main themes of OOL research and my general world view – which in itself - I like to believe has a rational and defensible origination. The simple story is that the biology, micro-biology research of the last 50 years are continuously unveiling levels of complexity over levels of complexity. As a person with a math and engineering education, I could not reach but a single firm conclusion: that our world is a DESIGNED world, that the LIVING WORLD is a DESIGNED world. We, normal human beings are looking for models, heroes and persons to admire and idolize. Is only rational for a human being like me to remain in awe to the Universe around us, to the Galaxies, our Living Planet, our animal, plants and human beings that populate this world. It is also human to recognize the single Person that deserve to be admired, revered and adored: is the Designer of this wonderful world, our Most Excellent God, our Most Excellent Engineer. I try to show to you that by a honest, rational approach, a human being can arrive to the idea of God – the Supreme Creator and Designer. I happen to be lucky to be born in a Christian family and to get a personal acquaintance with this God – and He fully deserve our worship! For me real science is just revealing new aspects, details and layers of the magnificent Creation, uncovering things left there by the Creator to direct our attention to Him and His Omniscience and His Omnipotence and His Benevolence.InVivoVeritas_{October 19, 2011
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I would suggest from a slightly different perspective the following: 1. The cell can be seen as a harmonious, intricate, coordinated composition of “hardware” and “software” elements. The plain existence of the cell as an exquisite assembly of hardware and software makes an even stronger argument that it was DESIGNED. 2. The hardware parts are constructed from atoms, cells, molecules, proteins, enzymes, cell organelles, nucleus, protoplasm, membrane - listing them in an increasing level of composition and organization. These hardware parts and their structured sets are used both as information storage, information communication and information processing support. They exist and manifest also as the material results of the cell processes: DNA replication, protein construction, cell development, cell division, etc. 3. The software in the cell may be presumed to drive many complex cellular processes: DNA replication, transportation, communication, cell division, immune reactions, chemical recycling, etc. It is not clear how much we understand the “languages” in which the cell software is expressed. 4. The miraculous thing is that the cell marvelous design is the basis of single-cell organism autonomy as well as one basic foundation for the autonomy of multi-cellular organisms. 5. The autonomy of the living world means a LOT: that the members of the living world can take care pretty much of themselves: they can feed themselves, arrange for intake of energy, can move to better places when needed, can sense and react to danger, can reproduce themselves, can exhibit tremendous flexibility, versatility and adaptability to external conditions. 6. There is no equivalent human-designed artifact that even come close in terms of the exquisite design and autonomy to the members of the living world. This clearly tells that the hypotheses that the Life originated through natural processes is totally unfounded in reason.InVivoVeritas_{October 19, 2011
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