Posted on 03/05/2002 9:45:44 PM PST by Southack
This is part two of the famous "Million Monkeys Typing On Keyboards for a Million Years Could Produce The Works of Shakespeare" - Debunked Mathematically.
For the Thread that inadvertently kicked started these mathematical discussions, Click Here
For the Original math thread, Click Here
Setting aside for a moment the question of whether going from a pile of lumber to a soapbox racer really meets this definition of the issue, let me tentatively accept it as you have stated it. ;)
The point is that while the natural selection theory of somatic change is plausible for features dependent on 1 or 2 genetic bit flips (like hair and skin color), more involved features involving many more SIMULTANEOUS coding changes CANNOT BE EXPLAINED using the bit flip (or as I put it the photomorph) explanation--because it is difficult to see what the intermediate steps could be.
Ah, but here you are assuming again that there must be simultaneous changes to produce a large-scale change. But many small changes over time can just as easily - more easily, really - add up to a large change. Consider the development of eyes. Your eye is a rather complex beastie (although not perfect, as our blind spots and my glasses remind us), and were we to posit a creature with no eyes suddenly and in one fell swoop developing eyes as you and I have them, we would be quite right in dismissing that possibility as ludicrously improbable.
Fortunately, there are intermediate steps, some of which we can observe in extant creatures. Many ticks, for example, have no eyes. But what they do have are rather primitive light-sensing cells in their skin. It's not much - just enough to tell the difference between light and dark. If you think of this as a a sort of proto-eye, you can see it's an extremely simple change from total blindness. It's not a huge leap, but it is a small improvement. Telling the difference between light and dark can give you an advantage over your blind competitors, so it is selected for. If you can tell the difference between light and dark, you will be more successful and leave more offspring, and eventually your blind competitors will be driven out by dint of your superior abilities.
Now imagine a development like this millions of years ago - not hard to do, as fossilized ticks more than 90 million years old have been found, essentially unchanged from ticks of today. So then, there's a small change from blindness to the ability to sense light. And over time, many small changes of this nature continue to add up. Cells that can sense light gradually migrate over bodies to gather in one or two particular spots. Why? Well, because having one or more light-sensitive cells in the same place allows you to begin to parse out some sort of detail about the world around you - vage and fuzzy detail, to be sure, but it's still better than just knowing the difference between light and dark. So, what was just a bunch of light-sensitive cells spread all over a creature's body gradually, and in small steps, becomes a cluster or two of light-sensitive cells. And these are what are called "eye spots", and you can still see them on primitive contemporary creatures like flukes.
And because having eye spots is better than just having light-sensing cells on your skin, it will confer an advantage to creatures who have eye spots. In an environment where creatures with eye spots compete with creatures with simple light-sensing cells, the eye-spotters will outcompete the light-sensors, and leave more offspring, and eventually drive out the competition (or force them to evolve also, of course).
And on and on, in baby steps, each step a small but noticeable improvement over the last. And it's just this sort of small, stepwise change that, over time, adds up to what we might call macro-change. At no time do any of the creatures in the progression have what we might consider a non-functional trait - they don't function nearly as well as your eyes do, to be sure, but it's not like they have half an eye. They're never sitting there with a retina and an optic nerve, just waiting in the dark for a cornea and a lens to evolve so they can finally see something.
Small changes over long periods of time are how macro-change comes about. Like I said, you're quite right to dismiss the possibility of seriously complicated traits or behaviors or anatomical structures arising in one step, since the odds would be absurdly long, and you'd most likely never see it happen in the entire history of the world. Fortunately, we all didn't have to rely on such a series of improbable events for us to come about. Certainly, as you say, the intermediate steps may be difficult to see, but it would be a rather boring universe that had its limits determined by the limits of our imaginations. ;)
Only in a trivial sense is a DNA coding sequence coding for a protein similar to software.
DNA as a 3 dimensional structure with functions based on this structure and built-in redundancy and infidelity. The interpretation of the sequence is entirely dependent on its environment and never in a binary sense.
What do you make of this? The conclusion I draw is that the space of biologically useful amino acid sequences is much larger than you suggest.
How would we know? It's not very often that someone goes to the doctor because they're too healthy.
The PROPORTION of useful sequences must be small.
Small has no absolute meaning. I think it can't be too small or that random string of amino acids wouldn't have been a useful enzyme.
Mutations generally are harmful.
My understanding is that most mutations are neutral. Of the remainder more reduce fitness than improve it in a well adapted organism, but there are more of the latter than you think.
It shows one of the fundamental differences.
There is a beneficial effect of low levels of ionizing radiation. Above a threshold there is a linear dose response of damaging effects.
But nevertheless, I think the problem you have now is that you've painted yourself into the corner of the fallacy of argument ad ignorantium, the argument from ignorance - because it has not been definitively proven true, it can be assumed to be false. Or, more precisely, because you can't imagine a path, there is no path. But, as I alluded to earlier, the limits of the universe are not determined by the limits of our imaginations.
What can I say? Examining the differences between eyes of various members of the animal kingdom, combined with what we know from the fossil record about when they arose on earth, can lead us to plausible pathways for the development of mammalian eyes.
So, here's one possibility, complete with real, live examples of each step. Simple photoreceptive cells, a la ticks -> eye spots consisting of multiple photoreceptive cells; e.g., flukes -> compound eyes composed of multiple photoreceptive cells differentiated into discrete units, viz arthropods -> simple pinhole eyes, with multiple photoreceptive cells differentiated into discrete units forming a retina behind a pinhole aperture; e.g., nautilus -> simple lens with variable focal length sitting in front of multiple photoreceptive cells differentiated into discrete units which form a retina, viz fishes and snakes -> fixed focal-length eyes with variable density lenses sitting in front of multiple photoreceptive cells differentiated into discrete units which form a retina, a la reptiles and birds -> further differentiation of discrete units of multiple photoreceptive cells which form a retina, such that discrete units exhibit variable responses to external stimuli in order to enhance image reception in low light and provide differential responses to varying wavelengths of light (i.e., color vision), A/K/A mammalian eyes.
;-)
I can't prove it, but I believe the answer is no. Certainly with the current state of technology the answer is no.
Since DNA was discovered, it was assumed to be a blueprint -- there were dogmatic statements about the one to one coding of genes and proteins. Now we are in something of a quandry, because there aren't enough genes to make this one to one mapping.
This is an empirical question, but an unsettled one.
My skepticism is based on experience with software design. With computers you have an environment in which every possible instruction has a completely defined effect. Yet it is difficult to design software that is reliable. Even worse, it isn't possible with the current state of technology to automatically translate a program from one delelopment language to another, or automatically port a software system from one Operating System or CPU to another. These tasks all involve finite lists of operations, but are too complex to automate.
I'm not convinced that it is possible to predict all the interactions that occur when DNA is "decoded".
It has been more than a century since Darwin -- who had no concept of genetics or DNA -- and the best gusee as to how life works is still variation+overproduction+selection. This is a pretty sloppy way for a computer program to operate, hence I maintain there is a fundamental difference between DNA and current computer programs.
The genotype-phenotype map that js1138 is talking about is something completely different. A frameshift mutation changes the genotype but does not change the relationship it has to phenotype. Phenotype is determined by a number of post-transcription events such as RNA-editing, alternative exon combinations, post-translational alterations, etc.
In any case, the most interesting states - the ones not currently well-understood, anyway - are a result of the tertiary and quaternary structures formed under various conditions. It's just my guess, but I'd bet that there will turn out to be a finite number of functional states, in terms of tertiary and quaternary structures, for a given genome.
You are right that it's long been a dead letter but it has nothing whatsoever to do with frame shift mutations. Anyway, I hope that some of your good argument is sinking in with "maro".
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