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

No. Membranes themselves are selectively permeable. This is easily demonstrated in the lab. No parts list. No memory. Just the properties of the membrane. Don't even need pores.DrREC_{October 19, 2011
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Thanks to BA77 and InVivoVeritas for answering a nagging question. I was wondering where this visceral reaction against origin of life research comes from. Other posters described it as "irrational" and "Wasted money. Wasted time. Wasted science." You called a Nobel laureate "extremely naive and uneducated." But now I get it: "a man would deny the source of all life, God, all the while severely deceiving himself and others that he can create ‘simple’ life without any need for God whatsoever???? " I hadn't brought up religion. I don't know Szostak's beliefs. But apparently you are threatened by this research. I understand your reaction better now. I also don't think anything I say, or the progress of the field will impress you much.DrREC_{October 19, 2011
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DrREC, In your reply you mention: "Nutrients and wastes can selectively pass, without a ‘parts registry’-…..” Which is a contradictory statement in itself. If the nutrients pass “selectively” as you say, isn’t that logically equivalent to saying that only a “selected list of nutrients” are passing through the pores? And that “selected list of nutrients” is reasonably called a “nutrient registry” in an informational lingo that hints also to the fact that there is some kind of Memory So, to make the absurdity of your statement more clear, let’s reformulate it: “Nutrients can selectively pass without practically conforming with a selection list of nutrients” Now if, for example, the membrane has two type of pores: P1 - having a triangle shape of size S1, the other P2 having a pentagon shape of size S2 and there are only two “good” nutrients that can “pass” through these pores because nutrient N1 has a triangular cross-section of a S1 size and the other nutrient N2 has a pentagonal cross-section of the S2 size, this, logically is still equivalent with a “nutrient registry” located at the membrane level. The big questions here are: 1. How come that the cell developed a triangle-shaped pore P1 that matches perfectly the shape and size of the good nutrient N1? And the same for pore P2 matching nutrient N2? 2. How come that the nutrient N1 passed by the pores of type P1 is also a “good” nutrient for the cell, i.e. it happen to feed the metabolism of the cell? 3. Was any “coordination” or intelligence manifested in the nature of N1, its size and shape and the “construction” of the pores of type P1? It is very hard to accept that so numerous MATCHES, COINCIDENCES that can be observed in the structure, composition of a cell in cell bodies and their coordinated functionality is the result of random processes and random occurrences.InVivoVeritas_{October 19, 2011
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I think Dr. Liddle has a point if she means the hardware and the firmware are essentially the same thing, just as it is for computers. Although software can be built atop, the founding layer of instructions is simply the byproduct of electricity passing through the chip's physical architecture. Thus if you want to change the instructions at the lowest level, you must do so by creating a new chip with a different architecture (excluding field-programmable gate arrays). Deciding which functions of the cell are analogous to firmware or software is another matter.rhampton7_{October 19, 2011
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InVivo, I,m sorry, perhaps I wasn't clear, I was directly addressing DrREC, and was not addressing you save only to compliment you for your post!bornagain77_{October 19, 2011
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bornagain77 I am sorry that you misinterpreted my blog entry. I really wrote that entry just to start illustrating the arrogance of scientists believing the materialist Creation Myth. I guess my point was not clearly made! However, I was preparing to reply to DrREC on the same line with your line: I might be arrogant to qualify Nobel laureate Dr. Jack W. Szostak as ‘uneducated’ (and maybe my choice of words was bad) but isn’t he much more arrogant to – as you say – “deny the source of all life, God” ?InVivoVeritas_{October 19, 2011
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InVivo, though the information processing is missing, here is a video that goes well with your rough sketch:
Cell Membrane - video http://www.metacafe.com/watch/895198/
As well, seeing that Szostak's very own work testifies against him ever finding functional proteins, It is safe to assume that he is operating on imagination instead of any rational evaluation of evidence that life could have arisen materialistically;
Szostak on Abiogenesis: Just Add Water - Cornelius Hunter - Aug. 2009 Excerpt: "While Szostak and Ricardo may sound scientific with their summary of the abiogenesis research, the article is firmly planted in the non scientific evolution genre where evolution is dogmatically mandated to be a fact. Consequently, the bar is lowered dramatically as the silliest of stories pass as legitimate science." http://darwins-god.blogspot.com/2009/08/szostak-on-abiogenesis-just-add-water.html
Even the low end estimate, for functional proteins given by evolutionists (1 in 10^12 Szostak)), is very rare:
Fancy footwork in the sequence space shuffle - 2006 "Estimates for the density of functional proteins in sequence space range anywhere from 1 in 10^12 to 1 in 10^77. No matter how you slice it, proteins are rare. Useful ones are even more rare." http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-328.html
It is very interesting to note that the 1 in 10^12 (trillion) estimate for functional proteins (Szostak), though still very rare and of insurmountable difficulty for a materialist to use in any evolutionary scenario, was arrived at by calling a binding/sticking of ANY random protein to the 'universal' ATP energy molecule, a functional protein. It is severely misleading of Szostak to say 'sticky' proteins are functional to put it very mildly.
How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html
The entire episode of Szostak’s failed attempt to establish the legitimacy of the 1 in 10^12 functional protein number from a randomly generated library of proteins can be read here:: https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-2/#comment-358394 This following paper was the paper that put the final nail in the coffin for Szostak's work:
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
Further notes:
On The Origin Of Life And God - Henry F. Schaefer, III PhD. - video http://www.metacafe.com/watch/4018204 "The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. http://www.us.net/life/index.htm
Music and verse:
John 14:6 Jesus answered, "I am the way and the truth and the life. No one comes to the Father except through me. Steven Curtis Chapman - God is God (Original Version) - http://www.youtube.com/watch?v=qz94NQ5HRyk
bornagain77_{October 19, 2011
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InVivo, very good for off the top of your head? DrREC and you don't find it the least bit arrogant that a man would deny the source of all life, God, all the while severely deceiving himself and others that he can create 'simple' life without any need for God whatsoever???? Perhaps we should back up a little and take things one step at a time since you seem to think the job for God is up for grabs,, shall we??? Can you please cite just one experiment where a single photon was created from absolutely nothing???
One day a group of scientists got together and decided that man had come a long way and no longer needed God. So they picked one scientist to go and tell Him that they were done with Him. The scientist walked up to God and said, "God, we've decided that we no longer need you. We're to the point that we can clone people and do many miraculous things, so why don't you just go on and get lost." God listened very patiently and kindly to the man and after the scientist was done talking, God said, "Very well, how about this, let's say we have a man making contest." To which the scientist replied, "OK, great!" But God added, "Now, we're going to do this just like I did back in the old days with Adam." The scientist said, "Sure, no problem" and bent down and grabbed himself a handful of dirt. God just looked at him and said, "No, no, no. You go get your own dirt!" http://www.getyourowndirt.com/
bornagain77_{October 19, 2011
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Maybe instead of picking one line from an interview, and concluding someone is "extremely naive and ‘uneducated," you could read his publications, summarize them, and critique his research or the state of the field.DrREC_{October 19, 2011
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"In conclusion, Mr. Jack W. Szostak – the Nobel laureate – seems to be extremely naive and ‘uneducated’ about the complexity of the task he started on about 25 years ago: to figure out the origin of life." That is Dr. Jack W. Szostak, and man what arrogance! Just so you know, Szostak has multiple publications experimentally probing the permeability of model membranes. Nutrients and wastes can selectively pass, without a 'parts registry'-which isn't really how most pores operate (although there are some specific transporters). Other suggestions-such as motility, chemotaxis, advanced cell signaling, and a circadian clock aren't even found in all modern life!DrREC_{October 19, 2011
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Yes, kf, but what some of us are saying is that that's where the analogy simply breaks down. You can't "load software" into a molecule the way you might "load software" into a digital computer. The molecule is what it is.Elizabeth Liddle_{October 19, 2011
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Here is the Quote from the Jack W. Szostak interview: "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. The part we’ve come to understand reasonably well is the membrane part. The genetic material is the harder problem; the chemistry is just more complicated. The puzzle has been understanding how a molecule like RNA can get replicated before there were enzymes and all this fancy biological stuff, protein machinery, that we have now in our cells." I am a software engineer with tens of years of experience of implementing software systems. A sane software engineer when given a new project, it has a well defined approach for taking the project from a starting idea to the final, working product. One of the first steps of this professional approach is to write a "Requirement Specification" to clearly, neatly and accurately specify each and every demand that need to be fulfilled by the final product. I thought that it would be very instructive to only START sketching such a "Minimum Requirements Specification for a Most-Primitive Life Form" and after a first sketch to compare notes with Mr. Jack W. Szostak statements in his interview. Below you can find the first iteration of such requirement specification, and detailed (somewhat, but not too much) only for the first of the eight major requirements. Please do not forget, that this is the first write up, produced with not too much thought - where I am sure I may have missed many other major requirements. Some conventions: - we will call this "most primitive" form of life a "cell" - for convenience - we will call the needed boundary of this 'cell' a 'membrane' Here is the Initial Requirement List: 1. The cell must have a physical boundary around its volume to clearly delimit the inside of the cell from outside of the cell. Let's call this boundary "membrane" List of minimum requirements for the membrane of the cell 1.1. Must provide reliable isolation of the cell content from the outside world 1.2. Must be "permeable" to specific materials or sources of energy that "feeds" the cell 1.3. Must have 'substance recognition' capabilities in order to allow or prohibit admission inside the cell of the good respective bad 'materials' (sensory capability). 1.4. Must have 'open gate through membrane' and 'close gate through membrane' reactions and mechanisms to open 'pores' (openings) in the membrane when good versus bad 'materials' are recognized outside or inside the membrane (reactive capability). 1.5. INFORMATIONAL SUPPORT PERSPECTIVE: 1.5.1. The membrane must exhibit a capacity to store and process information locally about the nature/identity of the good materials as well as about bad materials. Logically that is equivalent with a 'registry' of good/bad materials. 1.5.2. Pattern recognition: the membrane must have pattern recognition informational capabilities to accurately recognize any 'material' (or 'material pattern') that is available in its own 'registry' memory and to send appropriate signals to the control agents in the membrane when such materials are detected in its external or internal environment. 1.5.3. The membrane must have a set of control mechanisms on how to react to an 'inventory' of stored information of good and bad materials, in particular on what membrane 'pores' to open or to close when particular materials are identified. 1.5.4. Most probable the membrane should have ability to 'communicate' information/signals to the inside the cell when material 'signatures' are detected. (information communication and signaling) 2. The cell must have mechanisms to feed itself from outside world with specific substances that provide food/sources of energy for the (metabolism) processes that animate the cell. 3. The cell must have mechanisms to replicate itself into one or more similar descendent cells that exhibit the same behaviors and capabilities as the mother cell. 4. The cell should/may have mobility in order to leave a world environment that it detects as unfavorable and move toward other areas of the environment that are more favorable to its continued existence and proliferation. 5. The cell should/may have mechanism to 'sense' its environment and to 'react' accordingly. To 'recognize' 'favorable' conditions/elements in its environment as well as 'recognize' unfavorable conditions/elements in its environment. 6. The cell must have ability to transform the raw materials/energy received from environment through its membrane and transform them into different type of materials that are proper for its own internal 'construction' projects. 7. The cell should/may have capability of identifying 'refuse' materials resulting from its material transformation and conversion processes and forcing these 'refuse' out of the cell through the membrane to outside world. 8. The cell should/may have time measuring / time signaling capabilities in order to control its own material input, material transformation, material output and cell replication processes on specific timelines and coordinated schedules. I develop to the next level of detail only the 'membrane requirements' for this 'most primitive' form of life. I guess that some serious thought on these major requirements will distil into somewhat unexpected - but logically defensible - lower level requirements that involve information processing, material transportation, information communication inside the cells - that, together will construct an objective picture of the REAL COMPLEXITY that would be required for such a MOST PRIMITIVE FORM OF LIFE. What is not immediately apparent for anyone is that the living world and all its members manifest - it's true, in a varied degree - the "autonomy" characteristic which is another name for ‘viability’ ‘survivability’. This autonomy capability is extremely complex, demanding and multi-faceted and is also "extremely expensive" to "implement" by a designer, by evolution or by any entity. Let's do not forget that humankind in its most advanced state of technological progress, was not ever capable of dreaming to construct any artifact to an approaching level of autonomy - as it is routinely end richly encountered among the members of the living world. In conclusion, Mr. Jack W. Szostak - the Nobel laureate - seems to be extremely naive and 'uneducated' about the complexity of the task he started on about 25 years ago: to figure out the origin of life.InVivoVeritas_{October 19, 2011
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“Software” = “Information.” Equating the two seems like a stretch. But the point of the original post, and my objection was the use of hardware vs. software in the analogy. If we describe hardware as the physical medium of a computer, and software as what runs on it, how does this relate to early life? Is a self-replicating set of polymers hardware or software? It just isn't a meaningful analogy, and calling out EL for pointing that out isn't meaningful either. "information is not a property of the matter in which it is encoded." The sequence of protein or RNA produced by DNA is a direct consequence of the order of the chemical bases on the DNA.DrREC_{October 19, 2011
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Barry, you misundertood me. Joseph said: "Yup, perhaps 1/2 way there pertaining to the hardware (big maybe) but pertaining to the software scientists haven’t even started." My response, that the hardware is the software in a cell assumed that Joseph was not simply talking about the lipid vesicle membrane by "hardware". That isn't "hardware" by any analogy with a computer - that's just the case. The "hardware", therefore, has to be the polymers enclosed in the vesicle. But there is no additional "software" that has to be installed on that "hardware" The molecule is both software and hardware.Elizabeth Liddle_{October 19, 2011
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Joseph, I went to your blog and after reading the post you had linked to I started to look around. It seems you use you blog as a forum to threaten others with violence, abuse them in the most disgusting ways and generally act in quite a different manner to which you comport yourself here. Why is that Joe? Why?kellyhomes_{October 19, 2011
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Jack Szostak says: “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” What, exactly, is the property of the genetic material that is so important? It’s the stuff that gets “replicated and inherited.” And why is it important that there be something that gets “replicated and inherited”? Szostak again: “You want something that can grow and divide and, most importantly, exhibit Darwinian evolution.” The sine qua non of Darwinian evolution: Information! We are not talking about something that is “analogous” to information. We are talking about information. “Software” = “Information.” And no matter how you slice it, information is not a property of the matter in which it is encoded.Barry Arrington_{October 19, 2011
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"No transcription, and no translation of the mRNA codons in the ribosome to make proteins in a step by step AA sequence." We're discussing origin of life scenarios. You've given me a litany of the stuff of a modern cell: Transcription (DNA) and translation, mRNA, codons, ribosomes, and proteins. I'm betting Jack Szostak thinks those came later.DrREC_{October 19, 2011
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"1- There aren’t any self-replicating RNAs." I'd disagree with that, and I think you're trivializing the research. It doesn't really matter to the discussion here. 2- That ain’t proto-life Not alone, but an important proof of principle. "3- In order to repair something you have to know A) it is broken and B) how to fix it" "you have to know" is really inserting agency in there, isn't it. Enzymes like Photolyase can physically recognize change to the DNA structure that mispairing, or DNA adducts cause. It is a physical recognition, independent of what the DNA codes for. These are enzymatically reversed. They can also be removed, and the strand repaired, using the DNA bases on the other strand as template. 4- Without that you don’t have first life Who says first life had to be accurate/repairing?DrREC_{October 19, 2011
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Software is where EXPLICIT, prescriptive, functional info gets loaded into a digital system. if you want to deny the reality of that FSCI, then it make sense to pretend that there is no software in DNA, just chemicals in a strange polymer. No transcription, and no translation of the mRNA codons in the ribosome to make proteins in a step by step AA sequence. And most of all no von Neumann self replicator in the living cell. NOT!!!!kairosfocus_{October 19, 2011
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"Because life replicating is about informational coded instructions for replication, " And is that hardware or software, in the hypothetical case of a closed catalytic pool of RNAs that can catalyse themselves and other reactions? Is each RNA the hardware or software? "Well it’s your religious belief, not mine. It’s not up to someone else to prove your religious worldview to you. That burden is your responsibility." I'm finding it harder to have a discussion here without having some odd rambling about my religious worldview tacked on. Seems like a default, when you have nothing better to say. I'll ask the question again: "In the combustion of hydrocarbon by oxygen to produce carbon dioxide, water, heat and light, what is the hardware and software? Silly, isn’t it?"DrREC_{October 19, 2011
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DrRec: "Analogies are only useful to a certain point. In this case, dwelling on the “software” versus “hardware” of early life obfuscates rather than clarifies." ==== Obfuscates ??? Hardly. The Software question is the number one important point of discussion that should always be dealt with first and foremost, but we all know why it's one of those subjects that needs muddling in any discussion. If the Miller/Urey experiment had created informational codes, then that would have certainly provided all the proof your Church needs for an arguement. ----- DrRec: "What meaning does hardware or software have to self-replicating RNAs, or a pool of molecules that collectively has catalytic and self-replicating properties?" ==== Because life replicating is about informational coded instructions for replication, not some stupid blind luck of lightning from a Volcano striking a toxic waste chemical cocktail pond found in some mythology. ---- DrRec: In the combustion of hydrocarbon by oxygen to produce carbon dioxide, water, heat and light, what is the hardware and software? Silly, isn’t it? ==== Well it's your religious belief, not mine. It's not up to someone else to prove your religious worldview to you. That burden is your responsibility.Eocene_{October 19, 2011
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Joe, nitpicking doesn't help here. A. change to the sequence can result in a change to the instructions "With large proteins that require chaperones you can change the sequence and still get the same result." Ok, not all mutations disable function, and chaperones help. "OR you can change teh sequence and have the ribosome reject it." No idea what you mean here. No idea what you mean here.DrREC_{October 19, 2011
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Dr REC:
Both sides are always templates for DNA replication, and either side can template mRNA.
When I wrote it I was stuill thinking "sense/ antisense"- well that is what I was taught too. But yes now we know both sides can code for RNAsJoseph_{October 19, 2011
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With large proteins that require chaperones you can change the sequence and still get the same result. OR you can change teh sequence and have the ribosome reject it.Joseph_{October 19, 2011
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"So this is how I envision DNA- both sides of the ladder carry redundant information. One side does the work, that is transfers programming data to other molecules it contacts (mRNA for example) and the other side is a template for DNA replication" Both sides are always templates for DNA replication, and either side can template mRNA. "These instructions are not the sequence, rather they are embedded on the sequence" Is physically a distinction without a difference. Change the sequence, and the "instructions" change.DrREC_{October 19, 2011
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1- There aren't any self-replicating RNAs. The best we have so far is two RNAs one for the template and one that can catalyze one bond between two other RNA sequences that form on the template. 2- That ain't proto-life 3- In order to repair something you have to know A) it is broken and B) how to fix it 4- Without that you don't have first lifeJoseph_{October 19, 2011
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"What self-replicating RNAs?" Those proposed by RNA-world advocates, and to some extent, selected for in laboratories. "or a pool of molecules that collectively has catalytic and self-replicating properties?" "Why does that require software?" So proto-life could be software free? Interesting? "OTOH transcription, translation, proof-reading, error-correction, editing and splicing require software OR agency involvement…" Again, the software analogy isn't helpful. DNA repair enzymes operate by shape-physically recognizing and correcting mismatches and bulges. That is software? And why do you think all those things are required for first life?DrREC_{October 19, 2011
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DrREC:
What meaning does hardware or software have to self-replicating RNAs,
What self-replicating RNAs?
or a pool of molecules that collectively has catalytic and self-replicating properties?
Why does that require software? OTOH transcription, translation, proof-reading, error-correction, editing and splicing require software OR agency involvement...
Joseph_{October 19, 2011
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As I said on my blog almost three years ago: Up to now biological information has always been related to the DNA sequence (sequence related). IOW the information depended on the sequence. I do not believe this is a tenable position. I say that because in biology we observe that DNA just doesn't replicate itself, it does so with the help of other molecules in the cell. Those molecules are constructed by the information stored in the DNA. That's right- stored in- as in the data that is stored in a computer's hard drive, ROM and RAM. And this is my point- that DNA, RNA and other cellular components are actually data carriers just like the computer components I just mentioned. IOW the sequence is not the information. The sequence is important to carry out the instructions, that is the information embedded in the DNA (and perhaps other cellular components). As I said in an earlier entry- Just for a eukaryotic cell to make an amino acid (polypeptide) chain- Transcription and Translation: You start with a tightly wound piece of DNA. Enzymes called RNA polymerases, along with transcrition factors, begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout. At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed. Both sides of the parent DNA are exposed yet the mRNA "knows" to only form on one. This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA. So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell. A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthetase is used.
There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-pg 23
And then the chain starts forming until the stop codon terminates the process. Next is the folding process. That is what allows the protein to be useful- its spatial configuration. That is just the basics of what one is introduced to when reading biology textbooks. And it doesn't include the proof-reading and error correction that accompanies the process. So this is how I envision DNA- both sides of the ladder carry redundant information. One side does the work, that is transfers programming data to other molecules it contacts (mRNA for example) and the other side is a template for DNA replication. Once DNA replication is complete the program is transferred to the newly constructed side via the hydrogen bonds that connect the two sides. When other molecules are made- mRNA for example- they are given their instructions via the same hydrogen bonds. That information consists of editing instructions, as well as configuraion/ assembly instructions and destination instructions. These instructions are not the sequence, rather they are embedded on the sequence, just as computer data is embedded on the disk. -----------------------------------------------------------Joseph_{October 19, 2011
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Analogies are only useful to a certain point. In this case, dwelling on the "software" versus "hardware" of early life obfuscates rather than clarifies. What meaning does hardware or software have to self-replicating RNAs, or a pool of molecules that collectively has catalytic and self-replicating properties? In the combustion of hydrocarbon by oxygen to produce carbon dioxide, water, heat and light, what is the hardware and software? Silly, isn't it?DrREC_{October 19, 2011
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