Information and Evolutionary Mechanisms

Neo-Darwinism/Modern Synthesis did not explain developmental processes or fully account for fossil evidence nor was gradual, step-wise point mutations w/selection sufficient to account for genetic change, abrupt, rapid, discontinuous bursts of evolution.  Instead of a single mechanism that tries to account for everything by natural selection and adaptation there are a number of factors at work.  Natural selection is still very important, but it can't explain everything and not every trait is an adaptation.  Evolution is more complicated.  Other processes are involved in addition to natural selection.  The goal of the Extended Evolutionary Synthesis (EES) is to accommodate these changes in understanding (the link gives more detail about these changes, including instructional videos).  

*I would sum up our understanding this way: the discoveries in the past few decades have reinforced the evidence for evolution and common ancestry and shown that evolutionary change is far easier to achieve than we thought, but has made the origin of life and origin of complex genetic mechanisms that allow for this change far more difficult to explain. 

Personally, I believe in the supernatural and find this supported by other evidence and personal experiences, but I also recognize that science can't prove/disprove the supernatural and don't especially like the term "intelligent design" because too much baggage is associated with it.  There are many professional scientists who are religious but also accept in evolution.  Francis Collins, who headed up the Human Genome Project is one such individual who accepts the evidence for evolution and is also an evangelical Christian.  He founded an organization called BioLogos that explores these issues.

Where did you see me write anything about a supernatural force? My point to you from my experience in design and coding, nothing happens without a cause. You want your car to go faster, you push down a peddle, and many things take place, propelling the car in greater speed. You want your house to cool down; you adjust your thermostat, and it cools. What automatically occurs due to code is because the coding was designed to act that way. At no time does the code act independently to take on some new task. If something causes additional or subtracts some code pieces from outside the code itself, it is either with or without intent. Both of those can cause bad things to occur, and one of them will always disrupt the function it was designed for.

That analogy doesn't work though for genomics as explained in my prior post 

I think all this demonstrates is how very limited some of the analogies we use are?

Living organisms are not organised & regulated according to a kind of 'organic computer code', at least not in the sense of any computer that humans have ever built.

Yes and no.  True, a lot of the analogies don't work but because they're too simplistic, rigid, and limited when compared to biological information systems which are actually far more complicated, far more sophisticated, and far easier to modify and change than any computer system we have today. 

But living organisms truly are organized and regulated by an "organic computer code" and the genetic code is only one of numerous organic codes in living things.  The nucleotide sequences in DNA and RNA meet the definition of linear, digital information.  The transcription/translation of this information by means of an intervening (genetic) code w/built-in redundancy is the same as information transfer through a Shannon Information Channel and the bits of information can be mathematically calculated.  And that's just the tip of the iceberg.  It truly is astonishing. 

A myriad of complex informational processing and regulating networked mechanisms in even the "simplest" cell make it easier for genome restructuring and altering to occur (i.e., easier for evolution to happen), but the trade-off is it makes the origin of these mechanisms and origin of life far more difficult to explain. 

There is an *intentionality* about living organisms/biological information--that is true--and it's difficult to see how to derive this from "mindless" (as @TruthMuse says) physico-chemical processes/reactions that lack this property.  Biological information is also not just simply Shannon Information, but is recognized to possess additional properties.  For example, genetic information is prescriptive in that it prescribes function. 

Prior to these discoveries we only knew of this type of information processing to occur via the intentional acts of free agents (humans), so I get that part of the analogy/reasoning (i.e., in our experience, the origin and processing of prescriptive information to achieve a pre-determined functional goal was only known to occur via intelligent human agency). 

The whole thing is also just highly problematic on a conceptual level.  For example, random chemical processes could theoretically produce a piece of paper with ink spots in just the right shapes and form to give us written instructions for a cooking recipe, but it still would not endow those spots with linguistic meaning.  Similarly, chemical nucleotides truly function as arbitrary, token symbols--and less like chemicals--that comprise a true representative symbol language in every sense of the word.  Information is instantiated into physicality but still abstract, non-physical formalisms at the core.  So deriving non-physical abstract formalisms (arbitrary symbol language codes with semantic meaning) from the physico-chemical world is a huge conceptual problem.

So, ID-proponents really do have a point on this.  I just don't know what science can do with it.  This could constitute a philosophical argument potentially (and, indeed, this issue is one of the reasons why atheist philosopher Antony Flew became a theist).  But on the scientific side, there is no real empirical test we can apply here.  Plus, science as a rule cannot posit supernatural causation.  So, ID attempts to push this past philosophy and into science, go too far (and they need to dial it back).

*BUT, even though science can never "go there" (supernatural), we still must be wary of simple "answers" and assumptions that "nature must have found a way."  That is the assumption in science, but it's been assumed for so long that scientists forget that and just accept it as a given, obvious factual truth.  But it has yet to be demonstrated and our research has closed the gap a tiny amount in some places while widening the overall gulf enormously.  We truly have no scientific answer for how to derive all this from natural physico-chemical processes.  That doesn't mean we go all god-of-the-gaps, but neither can we express any optimism here.

So do we need someone who will be for Biology what Einstein was for Physics?

I think it's even worse than that.  Einstein at least had Newtonian physics to build on.  This will require scientists from all fields (organic chemists are not enough) and that is already happening from geology to astronomy to atmospheric science to biology and chemistry and information theory to quantum physics.  Most biologists lack training in information theory and so those specialists have become vital.  Entire new fields have developed to study bioinformation including biosemiotics and biocybernetics.  Scientists of course don't ever like to say no solution is possible (statements like that also don't bring in research grants and paychecks!), but there are some who say it's impossible.  Information theorist/expert, HP Yockey, for example--an agnostic to his dying day--but effectively said not possible to derive these information systems from prebiotic chemistry.  Criticized prebiotic scenarios, showed how they don't work, made parodies equating origin of life scenarios w/Greek mythology.  Said life is unexplained axiom/postulate (which of course doesn't explain anything either).  Who knows, perhaps one day we will find a scientific/naturalistic explanation.  At present though that is merely a hope and faith position.

Okay. I misunderstood. I was caught up in the word “design” and along with the other things you were saying I thought you were referring to a creator (this the supernatural force) who “designed” the DNA coding of organisms and who was driving the changes in the DNA sequence. My bad.

I wanted to give that some careful thought before responding. I can't remember the situation being summed up quite so starkly but perhaps it behoves us to focus more on what we do know reasonably reliably?

That's to say that we know life began on what appears to be an unremarkable planet orbiting a mediocre star (in Cosmic terms) on a rather distant arm of a galaxy, one of many billions in the Universe. And having begun, life then took the form of single-celled 'sludge' for almost 1000,000,000 years before the next step was taken towards multicellular life.

From then onwards the development of life can be explained in naturalistic terms. If so much of the long development of life on Earth can be explained by natural causes, I think it's reasonable to lean towards an equally naturalistic explanation for abiogenesis itself?

At least until the jury's in.

@stephen_33

I'm finally catching up on topics I've been meaning to return to for days.

So, we're no nearer to understanding how life began & the more we do understand about organic processes, the more formidable the difficulty seems to get. But side-stepping the (as yet) bewildering process of abiogenesis, we can be very confident that we have a good working model in evolution, to explain the enormous diversity of living forms we see around us.

That's to say, an entirely naturalistic mechanism by which species change & adapt over long periods of time, without any need to resort to more 'unusual' forms of speculation.

I'm content with not knowing the answer to the origin of life at the present time & possibly for the forseeable future but those who insist on grasping at some explanation need to make the parts fit: However life began on our planet, the process that followed - spanning some 3000,000,000 years - was a natural one.

Well, that isn't really an argument against ID. If the cells have built-in mechanisms to do specific types of alterations, they can do it? Who would dispute if it was built to do specific things, those things could be done?

That wasn't the topic, was it? To produce something that was never there before means changing what is there while keeping all vital functions running. Adding specific codes to produce an arm or a wing from some lifeform that didn't ever have one means altering the code to make the new limb! Not to mention everything that comes with the new features must be incorporated into the lifeform to make it useful, not useless. It is harder to alter a lifeform transforming it into something else, then built one from scratch without a plan, purpose, and design in my opinion.

@TruthMuse   You're right, that wasn't the topic.  But who said I was making an argument against ID?  The OP was whether or not there are genetic mechanisms to originate new information.  There are.  The nice thing is we don't even have to argue about it.  It's a fact. 

(As far as the other things you mentioned like arms and wings and such, genetic alterations are only one factor in the equation.  We're discovering that a lot of these developmental/morphological changes involve regulation of gene expression and developmental timing that don't necessarily have to involve any changes in "code" at all.  All the different types of eyes that we find in the animal kingdom can be produced by gene regulation effectuated by a single, master control gene (Pax6) found in all animals.  A significant amount of phenotypic variation isn't even caused by genetics; look up *phenotypic plasticity*)

Adding and subtracting code to build anything is the only factor as far as I'm concern. If there are going to be additional limbs, then throughout the whole process of adding them, resources will be strained to accommodate all the new body parts. If evolutionary changes are the mechanism every step of the way, they must add to the functionality of the lifeform giving it an edge over all of those things that don't have these alterations. These issues remain over the top in ways all of this would go wrong, from breaking code that is set up to do one thing, and tweaking it so that it breaks down in small ways, to ending the life altogether. It's an unworkable process without a plan, purpose, and design.

Time is a great issue here too, how many changes are required to move from a one-cell life form to man? How often do they occur, how much time was available? If the rate under ideal conditions was met without even considering failures, is there enough time? 

@TruthMuse   But it doesn't matter if you think adding and subtracting code is the only factor "as far as you're concerned."  That's wrong.  It's not the only factor.  There's very little difference, for example, between the human and chimpanzee "code" (as you incorrectly call it).  What makes us different from chimpanzees is not that small % difference in "code" but how the SAME "code" that humans and chimpanzees share is processed.  There's more than enough time for all the genetic changes representing life's diversity to occur.  More importantly, we have evidence that these changes have, in fact, occurred (and at different times during earth's history; not at the same time according to some "common design").  Instead of saying the same things over and over again, why don't you try studying the research I've given you to correct your misconceptions so we can have an informed discussion.  You're like the dissenter who keeps saying "It's impossible to run a mile faster than four minutes!  It can't be done!  It simply can't be done!" when it already has been done and improved on from there.  You're debating questions that have been answered.  We already know it's occurred, now we're just fleshing out the details.  How do you expect me to take anything you say seriously when you won't even acknowledge the no-brainer that "bacterial DNA in plant cells must have come from bacteria"?

Coding is an exacting process, not a haphazard one where we can just throw out letters in the hopes they form a word, and then all of the words create a command to do specific jobs. Right off the bat in this statement, acknowledgments about random and sometimes preplanned pathways are spoken of. A built-in function to do specific things like altering this or within specific limitations are design terms and functions; therefore, they acknowledge that life itself has error checking. It has a structure that works towards an end to keep specific things moving forward, sustaining life. Random alterations within a preexisting code will not produce new previously unknown forms and functions before it gets damaged and destroyed. The only thing this sentence shows intent and ability to do the work is required, in my opinion. Without it, where did the ability to not breakdown come from? Having alterations to DNA occur simply by being exposed to an ever-changing environment isn't capable of the alterations required to build a new lifeform, let alone a new system within one. New code requires a coder!

"In the same way that species are not static, neither are genomes. They change over time; sometimes randomly, sometimes in preplanned pathways, and sometimes according to instruction from pre-existing algorithms. Irrespective of the source, we tend to call these changes ‘mutations’. "

@TruthMuse

And yet we have tons of empirical evidence that "new code" can and does arise via natural mechanisms.  But you've made it abundantly clear that you're not interested in knowing the facts, so there's no point trying to convince you.  Once again, why would you expect me, @PyriteDragon or anyone to consider what you have to say when you refuse to inform yourself of the facts and refuse to acknowledge what other people say, like your refusal to acknowledge the no-brainer that "bacterial DNA in plant cells must have come from bacteria"?  I can respect differences of opinion, but what I have a hard time respecting is someone who criticizes and accuses people of not listening to reason and logic, while refusing to hold themselves to the same standards.  How hard is it acknowledge the sound, rational, logical conclusion that "bacterial DNA in plant cells must have come from bacteria"?

I'm interested that what we can see today, and today code if changes itself to adapt it was because it was designed to, not because there was a lucky glitch that altered to code and making it adaptable to something not previously seen, encountered, or fix an issue the code that it wasn't designed for. You picking out specific ways that biology adapts at specific changes is not evidence, in my opinion, for anything other than what it is doing. The process is the only thing I'm concern with. Can it do what it is being credited for? My answer is no. If there is some relationship between bacterial DNA and bacterial as you are pushing, maybe yes or no, I don't care; it isn't important to me. Either answer does not mean there was a common ancestor between all life, only that there may be some relationship between the two. I believe in evolution changes; they are small, not the wholesale ones that a common ancestor requires.

As I've repeatedly said the process is accounted for and cells have genetic mechanisms that allow them to rapidly restructure genomes.  So yes, the process can do what it's credited for.  You however insist on keeping yourself in the dark.  When you say my picking out ways biology adapts is not evidence, you are once again showing you're not even listening as I keep telling you that most genetic changes are not the result of adaptation and positive selection.  In fact, I don't believe I have once "picked out ways biology adapts" and used as an argument.  You continue to attack a dead horse while I keep telling you biology has moved past all that.

As far a bacterial DNA in plant cells, you still can't give an answer, so I am still waiting.  The fact that you don't care about it does nothing to diminsh it's importance as evidence that plant cells have a past evolutionary history that includes the acquisition of bacteria in an endosymbiotic relationship and subsequent modification to form chloroplasts.  The fact that you only care about *process* is similarly irrelevant, because regardless of how it happened the evidence still shows that plant cells have this past evolutionary history.  So if you only care about process and reject any naturalistic mechanisms, then fine, more power to you.  In fact, for sake of argument let's go ahead and do that and say you're right naturalistic processes don't work.  There.  Done.  That still leaves us with bacterial DNA in plant cells, the presence of which we're still left to explain.   Under an intelligent design view that would seem to leave us with two options: (1) either the past evolutionary history of plant cells is the result of an intelligent designer, or (2) an intelligent designer has falsely made it look like plant cells have an evolutionary history. 

And by the way, most IDs now do, in fact, accept the evidence for past evolutionary history of bacterial endosymbiosis in plant cells.  So if proponents of intelligent design accept it, then why don't you?

On a final note, one of the problems with the YEC position is the vague language employed about only accepting "small" change evolution or "limited" evolution and rejecting "large" scale changes.  You don't even know what you really believe.  How much evolutionary change is too much?  And don't give me that vague micro- macro- nonsense.  I'm asking you to tell me very specifically where exactly the boundary is between acceptable and unacceptable change.  Don't speak to me of extremes of how you accept evolution within "kinds" but reject "goo-to-man" evolution.  YECs never specifically define what "kinds" mean and only speak in subjective terms of how such and such amount of evolution "feels" or "seems" like too much.  That's one of the great problems with YEC: they don't actually try to scientifically determine the so-called limits of evolution, but just play guessing games about it.

So please tell me very specifically how much evolution is too much?  Please tell me very specifically in biological terms what constitutes separate "kinds."  "Kinds" used to be equated with "species" but this has been largely abandoned, because most YECs now recognize that speciation and the origin of new species is a confirmed fact.  So where then do we draw the line if it's not at the species level anymore?  And on the basis of what evidence do you draw that line?

Talking to you about my complaints is akin to saying that you cannot speak English with your refutations coming to me in either English speech or written English text. I tell you that for specific tasks to be done with error checking must come from an agency with a purpose, plan, and design to protect. Your rebuttal is saying no, no because specific things within biology that error check makes sure specific things can occur. You refuse to see that specific tasks with exceptional specificity found within biology reveals ID is required instead of refuting anything against ID. It is meaningless to say the same thing over and over when your refutation is the very thing you are trying to refute.

I don't argue for the age of the earth being old or young; bringing that up is meaningless to this discussion. I don't care how much time you think there has been what is being suggested for life from non-life, then mutating into all the modern-day lifeforms today isn't going to help you; as I stated before, time if not the friend of evolutionary theory and common ancestry. I'm not telling what I feel about this; the likelihood of altering a code to change into something different while maintaining its viability is nill without a coder.

"No currently existing formal language can tolerate random changes in the symbol sequence which express its sentence. Meaning is almost invariably destroyed." - Murray Eden, M.I.T.