Being Opportunistic
by Steve PetermannMike's nice post on endosymbiosis reminded me of a common situation found in engineering/manufacturing firms. It's a common strategy for these companies to position themselves for quick response when unexpected opportunities arise. Those opportunities might come from new technology that could be incorporated quickly into existing products or even open up new product lines. Getting to market first is key. It could also come from customers wanting some novel design in a hurry.
In either case what these firms do is prepare for unexpected opportunities. How do they do that? They create modular components with standardized and flexible interfaces that can be integrated together easily in novel ways. They maintain an inventory of raw materials and components so when an opportunity comes around, they are ready. The challenging part is deciding what to keep in inventory and how much. Being too broadly ready and you have problems with inventory turnover and cash flow. Be too unprepared and you miss the opportunity. This takes intelligence and planning, but it often pays off.
The picture of the aerobic eubacterium being incorporated into a cell, struck me as a good illustration of a chance to be opportunistic. The cell could add new functionality quickly, if it is ready. Now I'm no biologist, but I've seen it said that there is too much "junk" in the cell or DNA to indicate design. To this engineer this "junk" reminds me of the inventory of parts companies keep on hand, just in case. To the untrained eye these parts indicate poor management until the day their engineers scramble out to the bins, punch out a novel design, whip up a finished product, and deliver to an anxious customer on time. Obviously the cell can't afford too much inventory or it becomes burdensome. It would take some intelligent planning. However, with the right mix of quantity and type imagine how quickly the cell could take advantage of symbiotic opportunities that might come its way.
August 30th, 2005 at 6:47 pm
Steve, you just proved what I just mentioned in another thread: perhaps we will need engineers and physicists to reshape evolutionary theory.
Would evolution tolerate a system that would not have an 'inventory'? It may indeed be as simple as you suggest. The junkyard of genes may then be the dormant back-up system. In extreme evolutionary situations, the rules for gene recognition may be loosened and the backup genes are activated.
How many times have you used MS-DOS to get your Windows 3.1 back up and running? An evolvable system that is able to generate extremely complex life does not allow for crashes. Everything produced in evolution must work almost instantly and should always function.
Comment by AdR — August 30, 2005 @ 6:47 pm
August 30th, 2005 at 8:40 pm
Mike and AdR seem to be hitting close to something similar to a pet theory of mine.
As I am certainly no biologist many here may be able to kick some gaping holes into this little theory - and if the refutation is simple enough that it makes sense to me I will be grateful.
If it's actually a decent theory and it belongs to someone else forgive me if I appear to be stealing.
It starts with a premise based upon the question: What if there is no junk DNA at all? How would we account for extra that 95% (or so)?
To use Mike's term: inventory.
Say there are 10 segments of DNA in question, and only one of them is considered to be a gene: ie, responsible for protein production. This gene is then identified, and the remaining 90% dismissed as junk.
Now, if environmental conditions change, and the organism is subsequently analyzed, it may be found to have "mutated". The specimens surviving in the new medium are found to be producing a new protein, which implies a new gene. The DNA is re-examined, and a gene, similar to, but not identical to, the previous 10% segment, is now found to be translated into a protein.
This would appear to be a new gene, or a mutation of the original. but is it possible that it is not? Couldn't it be that the surviving organisms are those which have "shut-off" the original gene and "turned on" a different one? The prior existence of the now obvious gene would have gone unnoticed as it provided no protein. There might always be 10 genes, but only one is detectable at any time, in any environment, due to its expression.
In many cases this expression might occur in response to environmental stimuli, but that may not always be the case. Alternatively, is it possible that many forms of the gene are switched on in each generation, but with the expression of the not-yet optimal genes being undetectable (or even deleterious) in normal circumstances?
Some hypothetical example scenarios come to mind:
1) A certain bacteria has gene A, which produces an enzyme to metabolize substrate A. It also has an activated gene B for metabolizing substrate B. But in the absence of substrate B, or perhaps owing to the preponderance of A, the enzyme for metabolizing B is either not created or is quickly lost. It would never be noticed by an experimenter.
In the presence of substrate B and absence of substrate A, the bacteria appears to have mutated a new gene for the required reaction, as the associated protein is now found.
2) Or, each bacterium has both genes, but only one or the other is activated during the development of said bacterium. This activation would be determined by the presence, respectively, of either substrate A or B.
3) Or, the population has a naturally occurring mix of bacteria fit for metabolizing either substrate A or B. In the absence of B, those bacteria die off and are undetected. When the conditions change, the B bacteria survive and the A die off. The population appears to have mutated/evolved due to the changing environment.
(This is an example of a theory of evolution I call "shooting the brunettes":
For fifty years you go into a village and kill all the brunettes. A researcher comes along at the end of the fifty years and remarks that the villagers have evolved a propensity toward being blond in order to avoid being shot.)
In none of these cases would it be necessary to propose a random, fortuitous, mutation to explain the presence of the "new" gene. Ten similar genes could be designed to perform ten similar jobs in ten different environments.
Any thoughts?
By the way, "Pez" is a disposable alias in case this proposal is so stupid as to cause my extreme humiliation.
Comment by Pez — August 30, 2005 @ 8:40 pm
August 30th, 2005 at 9:11 pm
I'm sorry.
I meant Steve, not Mike.
Good start.
Comment by Pez — August 30, 2005 @ 9:11 pm
August 31st, 2005 at 12:03 pm
I am educated as a biologist and have worked mostly as a software engineer. I can tell you from my perspective as an engineer that 1) yes a modular design would be consistent with intelligent design. And, 2) an unelegant arrangement of parts stuck together with chewing gum and bailing wire is also consistent with intelligent designers. This can occur, but is not restricted to, when they are under time pressure to meet market opportunities.
Most programmers today use high level programming tools: Microsoft Visual Studio not assembly language.
The modular interfaces in life would most likely be seen at the level of the tools used to create the components and need not be in the components themselves. A good programming tool will allow modular interfaces to be designed but generate tight, efficient machine code. As physical humans inspecting designed biological systems, we may only see the generated machine code not the high level design specification.
Another situation, of many, that might result in inelegant design might be a a situation in which engineers are asked to make a quick fix to avert a catastrophe (ie an extinction?, recovery from an asteroid strike?), and then not being given time or resources to come up with a better solution after the crisisis is past.
I think a lot of IDists think of God combining atoms into molecules with telekenesis but it might be useful to consider an advanced civilization of discarnate human souls with bureaucrats sitting in committee meetings and submitting functional specifications to engineering with requests for input into project scheduling. In this civilization, biological components might not be created through telekenisis but through a nanotechnology manufacturing process.
The important points are 1) that re-use of components which is touted by Darwinists as a sign of evolution is however entirely consistent with design, and 2) uglyness is in no way shape of form a proof of natural evolution.
Comment by herrkartoffelkopf — August 31, 2005 @ 12:03 pm
August 31st, 2005 at 12:20 pm
Two more points to add to my previous comment:
1) The attendees of the committee meetings are the deans of an underfunded community college.
2) My summary at the end of the comment reminds me of the illogic of Darwinists.
http://www.abc.net.au/pm/conte...
"… One of the things that makes evolution really quite a strong theory is that it explains a lot of exceptions, it explains the imperfection in the natural world, just as much as it explains perfection."
The author of this quote doesn't realize the bankruptcy of this argument. Whatever he finds, beauty or uglyness, supports "evolution". If it's perfect it supports evolution if it appears imperfect it also supports evolution.
http://dictionary.reference.co...*
'tautology
n 1: (logic) a statement that is necessarily true; "the statement `he is brave or he is not brave' is a tautology" 2: useless repetition; "to say that something is `adequate enough' is a tautology"'
It's an interesting example of drawing the target after the arrow hits.
Maybe this explains why the author of that statement doesn't accept specified complexity. He is so used to painting targets after the arrow lands that he believes everyone else does it too. Specified complexity doesn't work when he (mis)uses it so how can it work for anyone else?
I'm gettig a little off the topic of the original post now, but the quote above is as silly as this one:
http://www.latimes.com/news/op...
"Scientists look for natural explanations for natural phenomena."
If the phenomena is natural then of course the explanation will be natural.
http://dictionary.reference.co...*
"1 entry found for circular reasoning.
Main Entry: circular reasoning
Part of Speech: noun
Definition: a use of reason in which the premises depends on or is equivalent to the conclusion, …"
I used to think ID critics were either being disingenuous or hadn't read about ID, but I am beginning to think that the problem is deeper. If they don't understand simple logic, how can they hope to evaluate ID?
Last off topic point: The continual mischaracterization of ID in the press by supposedly educated critics is proof that ID needs to be taught in school.
Comment by herrkartoffelkopf — August 31, 2005 @ 12:20 pm
August 31st, 2005 at 3:38 pm
Pez, doesn't sound bad at all. If you would specify this in a theoretical framework (e.g. system flexibility) and find supporting evidence for it in the literature or produce them yourself (most genome databases are public), you have the ingredients for an article.
The mechanism that you propose can be one of the advantages of using a population. I see a population more as a transition to another design that can lead to an increased level of complexity.
With a procedural computer language you can create a limited complexity. Object-oriented programming gives rise to a new higher lever of complexity and we really need distributed system in order to reach another level.
A population would basically create robustness by error toleration.
Comment by AdR — August 31, 2005 @ 3:38 pm
August 31st, 2005 at 4:17 pm
AdR, thank you for reading and responding.
Please forgive me if this response, or one like it, shows up elsewhere, I hit "return" accidentally and lost it somewhere into cyber-land.
Your point about populations is exactly what I wonder about.
When a 'mutation' is discovered in an individual I think 'isn't it possible that this is just a rare, but naturally occurring version or allele in the population as a whole which is perhaps becoming more common as conditions change?'. Or isn't it possibly a gene that was previously dormant, turned-off or masked?
Are stressed bacteria really hyper-mutating, or are the stressed ones disappearing from the environment, leaving the newly selected?
As for your first paragraph, I am just a curious hack who really enjoys reading these blogs and getting the insight of those of you who know what you're talking about. I just can't help putting my two cents into the arcade once in a while.
Comment by Pez — August 31, 2005 @ 4:17 pm
September 2nd, 2005 at 5:48 am
MrPotatoHead, you should know by now that, according to Darwinist's logic, we are facing to options here: either evolution is a fact or evolution is a fact.
And yes, you are free to choose any one of the two.
But seriously, I suspect that sooner or later Darwinists will try to coopt ID claims in biology as…you guessed…part of some evolutionary process. You see theory is so plastic that it can account for just about any contradictory empirical data. I think that will be its ultimate downfall.
Comment by inunison — September 2, 2005 @ 5:48 am