The Digital Demise Of Darwinism

[CraigD]

I do not think that you will find me (or Behe) repeating a falsehood.

I hope no hypography member would intentionally lie in these forums, so hope that greylorn is not.

 

Michael Behe, however, is a willing and enthusiastic fellow of the Discovery Institute, which has been uncontestedly shown to have embraced what they term “the wedge strategy”, which seeks to discredit “materialistic science” and “replace materialistic explanations with the theistic understanding that nature and hurnan beings are created by God”. These goals (which I believe to be in many individuals’ cases well-intentioned) are not intended to further the accuracy of scientific theories, but to improve human society by making theism legally, socially, and scientifically dominant in it.

 

Behe and other Discovery Institute fellows and supporters lie when necessary to further their goals, which is to produce a better society, not better understand nature. They argue, with justification, that regardless of its objective accuracy, scientific materialism is bad for society, while theism, regardless of its objective accuracy, is good.

 

I believe people who do not share this moral position should not align themselves with Behe and his supporters. I believe people who do, but claim to be motivated only by a desire to understand aspects of physical nature, such as the origin of life, either misunderstand the goals and nature of people such as Behe, or are themselves lying in an effort to achieve its goals.

 

On the core subject of this thread, the question of whether abiogenesis is possible without artificial (whether from a god, a human-like artificer, or even a well-programmed machine) input (what Intelligent Design advocated term “design”), I think the issue cannot be entirely settled until our ability to mathematically model the physical systems involved in it about as well as we have in recent decades been able to model those of the solar system.

 

In the medieval period, many respected intellectuals believe the motion of the planets required “intelligent management” by angels, pushing them along their observed paths. Kepler’s publishing of his laws of planetary motion cast doubt, but didn’t widely discredit this view. Newton’s publishing of his laws of motion and universal gravitation further suggested that the motion of the planets could be explained as not requiring intelligence, but due to the slowness of mathematical calculations using them, could not exclude the possibility that, while the planets moved largely due to unintelligent inertia and forces, intelligent agents were still necessary to guide them to produce their observed motion. As astronomers for the next several centuries performed calculations successfully finding and predicting the motion of previously unknown bodies, the consensus that the motion of the planets involves no artificial forces became so dominant that the earlier “pushed/guided by angels” view was largely discredited. A strict skeptic, however, could not be entirely convinced of this scientific consensus view until the past few decades, when electronic computers enabled astrophysicists to calculate precisely how the past and future motion of mater in the solar system.

 

Biology, I think, is in a similar state now to astronomy between about 1700 and 1970 AD, except that its body of work is necessarily larger and more complicated than that of astrophysics. The scientific consensus is that the whole course of life on Earth, including its origin from non-biological processes, does not require artificial management. However, because we lack mathematical computational biological methods that can show this in silico, a strict skeptic cannot entirely accept this consensus, so can’t entirely discredit explanation of the origin of life on Earth being artificial.

 

In both these cases, which involve phenomena of similar duration (about 4,500,000,000 to 3,500,00,000 years) computational physics can be used in a final step needed to satisfying strict skepticism. In both cases, such computation would be unnecessary if people had been around for 4,500,000,000 and either been similarly long-lived or good record keepers, or if we were very patient, and able to travel to newly forming star systems and wait and watch for billions of years. We have neither been around that long or are that patient, however, so computation physics provides a way we can essentially witness processes longer than we’ve been around or are willing or able to wait.

 

Anti-materialism, pro-theism people and organizations like Michael Behe and the Discovery Institute have focused most of their wedge strategy on biology, rather than astronomy, because of this difference in the two disciplines’ computational modeling maturity. Few Intelligent Design proponents argue that the solar system could not possibly have formed without artificial manipulation. Were a good computer simulation able to show the appearance of life from non-living processes without artificial manipulation, Intelligent Design proponents would be less credible in their claim that this is impossible.

[JMJones0424]

I don't know therefore an invisible sky fairy did it is hardly a skeptical stance. This is our current best guess given our current knowledge, but we may be wrong, is a skeptical stance.

[Buffy]

greylorn,

 

I don't have time for a point by point refutation of your recent post, but I think none is really necessary.

 

It is clear that you are not familiar with the relatively recent new understanding of what was formerly known as "Junk DNA" and how it appears to work according to recent theories. This lack of familiarity with this new understanding is at the core of why you do not believe the arguments that I and others have presented here about the computational probability of rapidly evolving organisms.

 

The crux of this understanding comes in two parts:

 

• "Junk DNA" isn't "junk" but rather "alternate sequences" that are currently turned off. Early analysis of DNA seemed to show that these vast swaths of sequences had no effect whatsoever on morphology. When people looked closer, they noted that they actually were very similar to the active sequences, and there's been experimentation since that shows that there are changes that occur that turn these sequences on. To use a computer analogy then, these sequences are whole "subroutines" that represent very complex and extensive instructions on constructing highly differentiated "alternates" that explain Eldredge and Gould's Punctuated Equilibrium.
  
• It has also turned out that what causes these large segments of DNA to be turned on and off is a random change in just a handful of base pairs elsewhere in the DNA sequence. In the computer analogy, these few base pairs are like an IF-THEN statement.
  

 

The bottom line on this is that just as a computer program can do radically different things just because the user hits a "y" rather than an "n" because that one IF statement calls a completely separate subroutine, having a single base pair copying error can in fact turn on or off huge morphological changes in the resulting organism.

 

And that means that in probabilistic terms, base pair changes are very, very, very highly interdependent with vast numbers of expressed genes.

 

The only way that you get the results that you do, is because you don't recognize that this is how we now understand how DNA works.

 

Obviously, as CraigD points out, we don't know everything, but we do know enough that the computations that you and Behe put forth are in fact not based on a true understanding of how the mechanisms work. I won't call it a "lie", I'll say it's a misunderstanding on your part.

 

I will also admit with some amusement that I believe the reaction to this from you and QDog might be that this is further evidence for the argument surrounding "symbolism" and there for de facto proof of a creator or Beon or whatever, but that's a separate issue because that addresses solely your alternate theories.

 

So at this point, given that all the parties other than the two of you here sit on the side of conventional modern theory, it's going to first be up to you to get up to speed on these theories, and if you are interested try to develop proof that they are wrong if you goal is to backup the "irreducible complexity" argument.

 

The assumptions you make in order to support "irreducible complexity" are in fact false, and you're going to have to come up with a new and novel approach, something by the way, that Behe has never attempted to do.

 

Now as to your theory of Beons, it looks like it might be interesting, but you might want to start another thread, because that is a *separate* theory that will need to be proposed and defended.

 

 

Everything that irritates us about others can lead us to an understanding of ourselves, :phones:

Buffy

[Biochemist]

"Junk DNA" isn't "junk" but rather "alternate sequences" that are currently turned off. ..... these sequences are whole "subroutines" that represent very complex and extensive instructions on constructing highly differentiated "alternates" that explain Eldredge and Gould's Punctuated Equilibrium.

 

Nice to read you again, Buff. Wouldn't it have been more accurate to have said that this characteristic of DNA is "consistent" with PE, not that it "explains" it? The mechanism of action of (misnomer) "junk" DNA is indeed consistent with PE, but frankly was not even necessary. We could have already "explained" PE by the arithmetically increased likelihood of expression of recessive alleles in small, sequestered populations. It is easy (and likely) to suggest that significant environmental changes during those rare PE episodes drove small populations to be separated from larger ones. We can demonstrate that large existing code blocks can be suddenly activated due to small changes in the chromosome, or due to expression of a recessive allele. But neither of these mechanisms explain how a large block of code could be fully functional and not previously expressed. If the large blocks of code were previously expressed, we would be a lot less "punctuated". How did we get large blocks of functional DNA code that was never previously expressed? If you drop back to the "lots of permutations were not functional" argument, we surface that ugly probabilistic issue again. And that particular instance has a lot less interdependence in the calculation.

 

The bottom line on this is that just as a computer program can do radically different things just because the user hits a "y" rather than an "n" because that one IF statement calls a completely separate subroutine, having a single base pair copying error can in fact turn on or off huge morphological changes in the resulting organism.

 

And that means that in probabilistic terms, base pair changes are very, very, very highly interdependent with vast numbers of expressed genes.

 

Very true. But it is less true if large numbers of codons were not previously transcribed/expressed.

 

....We know enough that the computations that you and Behe put forth are in fact not based on a true understanding of how the mechanisms work.

 

Behe was not all that much into computation. That was more Dembski. Behe was suggesting that sudden arrival of complexity doesn't pass the smell test. I appreciate your dissection of the somewhat shallow court-of-law confrontation above. Behe's argument does not really "prove" anything. It just raises provocative questions. My assertion is that if someone rules out the provocative nature of the questions, that someone is ignoring an issue.

 

I will also admit with some amusement that I believe the reaction to this from you and QDog might be that this is further evidence for the argument surrounding "symbolism" and there for de facto proof of a creator or Beon or whatever, but that's a separate issue because that addresses solely your alternate theories.

 

I thought that was a weak argument for existence of a creator as well. But perhaps I just didn't understand it.

 

Everything that irritates us about others can lead us to an understanding of ourselves....

 

But what about those things that we wildly appreciate in others?

 

Bio

Edited June 1, 2013 by Biochemist

[Moontanman]

Behe was not all that much into computation. That was more Dembski. Behe was suggesting that sudden arrival of complexity doesn't pass the smell test. I appreciate your dissection of the somewhat shallow court-of-law confrontation above. Behe's argument does not really "prove" anything. It just raises provocative questions. My assertion is that if someone rules out the provocative nature of the questions, that someone is ignoring an issue.

 

 

Uh huh, and just what would those provocative questions be? And exactly what issues are being ignored?

[Buffy]

"Junk DNA" isn't "junk" but rather "alternate sequences" that are currently turned off. ..... these sequences are whole "subroutines" that represent very complex and extensive instructions on constructing highly differentiated "alternates" that explain Eldredge and Gould's Punctuated Equilibrium.

 

.... Wouldn't it have been more accurate to have said that this characteristic of DNA is "consistent" with PE, not that it "explains" it? The mechanism of action of (misnomer) "junk" DNA is indeed consistent with PE, but frankly was not even necessary. We could have already "explained" PE by the arithmetically increased likelihood of expression of recessive alleles in small, sequestered populations. It is easy (and likely) to suggest that significant environmental changes during those rare PE episodes drove small populations to be separated from larger ones. We can demonstrate that large existing code blocks can be suddenly activated due to small changes in the chromosome, or due to expression of a recessive allele. But neither of these mechanisms explain how a large block of code could be fully functional and not previously expressed. If the large blocks of code were previously expressed, we would be a lot less "punctuated". How did we get large blocks of functional DNA code that was never previously expressed? If you drop back to the "lots of permutations were not functional" argument, we surface that ugly probabilistic issue again. And that particular instance has a lot less interdependence in the calculation.

 

Awwww, I know you hate this theory, but are ya really going to use the semantically glossed over version of "it's just a theory?"

 

This theory of "junk DNA" is no more "not necessary" to Punctuated Equilibrium as the concept of curved space time was to Newton's Law of Gravity. No, the lack of it did not invalidate or disprove Newton, but had gravity not been obvious physical and everyday reality to most scientists, having an understood mechanism for WHY gravity works would have resulted in prolonged and expanded skepticism rather than rapid acceptance.

 

The whole unfortunate point of this thread is that, in spite of Einstein, we still have wacko conspiracy theorists who believe in Expansion Theory. And a lot of people--legitimate, non-wacko-creationist evolutionary scientists--dissed PE until a "mechanism" was found.

 

The reason why these "unexpressed" sequences exist at all is that they're copies of successful ones with minor changes. The problem here is that "unexpressed" is actually a function of the incredibly sparse fossil record. Were these sequences *never* expressed? Ha! No. They do indeed go through expression as *recessive* traits, and only become dominant traits at points where there is external change that causes those traits to be advantageous. Having a large library of these sitting around means that you can get Punctuated change because they're all sitting right there waiting to be made useful.

 

We just don't see these in the fossil record because the darn "genetic experiments" are virutally impossible to find.

 

What makes your argument absurd though is that we're now seeing this huge library of potential for dramatic change in species sitting there in organisms that have been very stable but who also have not had the evolutionary pressures needed to cause a change. While we may have not figured out exactly the mechanism here it's incredibly silly to say that there's no way that functional "currently unexpressed" (it's not "never ever expressed") has nothing to do with PE.

 

The bottom line on this is that just as a computer program can do radically different things just because the user hits a "y" rather than an "n" because that one IF statement calls a completely separate subroutine, having a single base pair copying error can in fact turn on or off huge morphological changes in the resulting organism.

 

And that means that in probabilistic terms, base pair changes are very, very, very highly interdependent with vast numbers of expressed genes.

 

Very true. But it is less true if large numbers of codons were not previously transcribed/expressed.

 

So really, no, it's not that the were never ever expressed at any time, it's that they were recessive and not visible in the greater population UNTIL an environmental change caused it to become dominant in the population.

 

Moreover the point you've avoided so far is that environmental changes that make recessive genes dominant result in feedback loops that encourage cascade changes in what is expressed, either unleashing co-located genes or encouraging related genes that in combination become environmental advantages. That cascading is what makes it all Punctuated.

 

Unfortunately on this topic, there's almost no convincing the unconvinced because effects like I have described are not intuitive and are not commonly subjects of direct experience. AI is an amazing area of research precisely because of it's tantalizing similarity to natural systems of all kinds, not just intelligence. If you're not predisposed to looking for anything other than "it's all random or it's all directed by a supernatural being" it's hard to see all the real-world, naturally occurring analogs that are all over the place if you only look.

 

....We know enough that the computations that you and Behe put forth are in fact not based on a true understanding of how the mechanisms work.

 

Behe was not all that much into computation. That was more Dembski. Behe was suggesting that sudden arrival of complexity doesn't pass the smell test. I appreciate your dissection of the somewhat shallow court-of-law confrontation above. Behe's argument does not really "prove" anything. It just raises provocative questions. My assertion is that if someone rules out the provocative nature of the questions, that someone is ignoring an issue.

 

I know that Behe is mathematically illiterate: he has indeed relied heavily on Dembski for validation of his sense of "smell". GIGO.

 

The only reason they're provocative is if you ignore all the evidence that the mechanisms are there. Behe is exactly the type I'm talking about above: yes, you need mechanisms to prove to folks like Behe that evolution--let alone PE--is a fact. Unfortunately they don't want to hear about mechanisms other than their own, because their goal is justifying their world-view, not finding any truths about the way the world works.

 

I will also admit with some amusement that I believe the reaction to this from you and QDog might be that this is further evidence for the argument surrounding "symbolism" and there for de facto proof of a creator or Beon or whatever, but that's a separate issue because that addresses solely your alternate theories.

 

I thought that was a weak argument for existence of a creator as well. But perhaps I just didn't understand it.

 

Yah the whole notion expressed earlier in the thread about "symbolism" is pretty darn confused, so weak, yeppers.

 

Everything that irritates us about others can lead us to an understanding of ourselves....

 

But what about those things that we wildly appreciate in others?

 

Well, yah, Buffy in "her purest finding an appropriate quote" form... Carl Jung for those of you too lazy to look it up.

 

I don't think Carl was discounting that either, but sometimes folks make it darn hard to appreciate them!

 

I do find it ironic that my spiritual beliefs are considered so apostate precisely because they're consistent with a notion that God did not and does not meddle. Seeking a designer when one is not required is kinda sad in my book. Asking to be "open minded" about not only the existence of one but insisting that that open mindedness includes redefining the nature of science is a desperate attempt by those who do not like the conflict between their experiences and their beliefs to deny those experiences and seek unreality as the "defined truth." For someone to insist that their denial of reality is somehow provocative is hardly ignoring anything.

 

Unfortunately it's become quite common recently to consider any statement to be equally valid as any other--and thus a valid mechanism for defining any two opposite postions a "controversy"--no matter how much evidence there is to invalidate one and not the other.

 

 

Truth is more of a stranger than fiction, :phones:

Buffy

[Biochemist]

Awwww, I know you hate this theory, but are ya really going to use the semantically glossed over version of "it's just a theory?"

Shucks. I was really hoping for a "welcome back" after a couple years. I missed you folks. Oh, well.

 

Not sure what you are talking about here. I have always been a PE advocate. Still am.

 

The reason why these "unexpressed" sequences exist at all is that they're copies of successful ones with minor changes. The problem here is that "unexpressed" is actually a function of the incredibly sparse fossil record. Were these sequences *never* expressed? Ha! No. They do indeed go through expression as *recessive* traits, and only become dominant traits at points where there is external change that causes those traits to be advantageous. Having a large library of these sitting around means that you can get Punctuated change because they're all sitting right there waiting to be made useful.

Nothing in the junk DNA mechanism gets around the probabilistic issues. We will have to accept that the vast majority of small changes to a set of genes result in dysfunction. And any new protein will be scavenged by the various internal cell police (e.g., the ubiquitin tagging system) to remove new proteins.

 

We just don't see these in the fossil record because the darn "genetic experiments" are virutally impossible to find.

I am OK with this point of view, but it is a faith position. You can't suggest that the absence of evidence is proof, even if there is a legitimate justification for lack of proof.

 

What makes your argument absurd though is that we're now seeing this huge library of potential for dramatic change in species sitting there in organisms that have been very stable but who also have not had the evolutionary pressures needed to cause a change. While we may have not figured out exactly the mechanism here it's incredibly silly to say that there's no way that functional "currently unexpressed" (it's not "never ever expressed") has nothing to do with PE.

Perhaps I should suggest that we have not demonstrated that they were expressed. And the timeframe (particularly for the Cambrian explosion) remains problematic in any circumstance. Further, the reduction in phyla in the last 500 million years does not fit very well with this framework either.

 

So really, no, it's not that the were never ever expressed at any time, it's that they were recessive and not visible in the greater population UNTIL an environmental change caused it to become dominant in the population.

I do understand the position. But we have things that we know:

 

1. 
    
   
2. Recessive genes are more likely to express in smaller populations (by arithmetic)
   
3. The Cambrian explosion (and a couple others) occurred pretty quickly. We also don't have the advantage of large offspring count or frequent regeneration cycles once we get to higher phyla. It is difficult to advance a dozen phyla or two in 250 million years.
   
4. We cannot demonstrate that the recessive genes were ever expressed. It is OK to assume it, but it is certainly an assumption.
   
5. Speciation and phylogenation seems to have slowed down in the last 500 million years. Even if high phyla slowed due to smaller offspring count and rarer breeding cycles, there is no reason that lower phyla could not have continued to "climb the tree". This just does not fit the framework well.

 

Moreover the point you've avoided so far is that environmental changes that make recessive genes dominant result in feedback loops that encourage cascade changes in what is expressed, either unleashing co-located genes or encouraging related genes that in combination become environmental advantages. That cascading is what makes it all Punctuated.

The more complex the cascade, the less likely.

 

Unfortunately on this topic, there's almost no convincing the unconvinced because effects like I have described are not intuitive and are not commonly subjects of direct experience. AI is an amazing area of research precisely because of it's tantalizing similarity to natural systems of all kinds, not just intelligence. If you're not predisposed to looking for anything other than "it's all random or it's all directed by a supernatural being" it's hard to see all the real-world, naturally occurring analogs that are all over the place if you only look.

I am not sure who you are addressing here. I don't fall into either camp.

 

I know that Behe is mathematically illiterate: he has indeed relied heavily on Dembski for validation of his sense of "smell".

Tell us what you really think. :)

 

The only reason they're provocative is if you ignore all the evidence that the mechanisms are there. Behe is exactly the type I'm talking about above: yes, you need mechanisms to prove to folks like Behe that evolution--let alone PE--is a fact. Unfortunately they don't want to hear about mechanisms other than their own, because their goal is justifying their world-view, not finding any truths about the way the world works.

I don't think I can speak for Behe, but he does accept common ancestry. I am not sure where he is on PE. I agree with you that his discussion of irreducible complexity is a little overplayed, but it still raises questions: We have large complex structures that did not seem to have time to be tested via niche pressure.

 

I don't think Carl was discounting that either, but sometimes folks make it darn hard to appreciate them!

Well, I appreciate you.

 

I do find it ironic that my spiritual beliefs are considered so apostate precisely because they're consistent with a notion that God did not and does not meddle.

I am not in that camp either. Certainly not that you are apostate.

 

Unfortunately it's become quite common recently to consider any statement to be equally valid as any other--and thus a valid mechanism for defining any two opposite postions a "controversy"--no matter how much evidence there is to invalidate one and not the other.

...And I am certainly not in that camp.

 

Bio

[Buffy]

Shucks. I was really hoping for a "welcome back" after a couple years. I missed you folks. Oh, well.

I did! In the other thread you posted to dear! Anyways, Hiya Bio!

 

Not sure what you are talking about here. I have always been a PE advocate. Still am.

I know that. But you've always insisted on agreeing with Dembski's "computationally implausible" theory, and over years of us arguing, it's been clear that you simply refuse to even acknowledge that his simplistic probability computation is absurd on it's face, nor do you make any attempt to learn anything about any of the mechanisms of self-organizing systems.

 

As you're a Biochemist, I know you've had the statistical education to understand dependent variables and the effect of Bayes Theorem on probabilities. If you don't, I hope to God that I've never bought any of your company's products.

 

In fact if you listen to the leading lights of "intelligent design"--while they don't actually disown him--they have basically abandoned Dembski and are now performing mathematical errors left and right in a furious attempt to show that both Bayes as well as Information Entropy (Shannon) and Information Complexity (Kolmogorov) prove the opposite of what they actually show, which is that the information in DNA is highly correlated and interdependent.

 

Bayes Theorem is really all you need to see that Dembski is rightfully laughed at, so I continue to be absolutely non-plussed that you keep saying that there are "probabilistic issues":

 

The reason why these "unexpressed" sequences exist at all is that they're copies of successful ones with minor changes. The problem here is that "unexpressed" is actually a function of the incredibly sparse fossil record. Were these sequences *never* expressed? Ha! No. They do indeed go through expression as *recessive* traits, and only become dominant traits at points where there is external change that causes those traits to be advantageous. Having a large library of these sitting around means that you can get Punctuated change because they're all sitting right there waiting to be made useful.

Nothing in the junk DNA mechanism gets around the probabilistic issues. We will have to accept that the vast majority of small changes to a set of genes result in dysfunction. And any new protein will be scavenged by the various internal cell police (e.g., the ubiquitin tagging system) to remove new proteins.

If every base pair in every sequence in every strand of DNA were "independent" none of the mechanisms you do believe in would work. DNA wouldn't actually instantiate morphology, scavenger DNA wouldn't know what to zap, proteins wouldn't know how to support replication, all because nothing would have anything to do with anything else.

 

Either you agree that there's stuff that correlates and therefore the elements are highly dependent--in which case Bayes applies and the "improbability" disappears into thin air, or you insist that all random changes are completely independent, in which case you also have to believe that it's a miracle that it works at all because it's all just random numbers.

 

Now as it turns out, that's exactly why Shannon and Kolmogorov have come into play, because they are useful for proving the level of correlation/complexity that can be found in DNA purely on the basis of computational analysis of base pair sequences. As with Dembski, you'll find a lot of bogus "reinterpretations" by charlatans of this analysis, using the Rovian "take your biggest weakness and accuse your opponent of it even if you have no proof."

 

It's pretty amazing to watch. But at any rate, if you're going to insist that there's a "probability problem" you need to catch up with the times: you sound SO last millennium, dear.

 

We just don't see these in the fossil record because the darn "genetic experiments" are virtually impossible to find.

I am OK with this point of view, but it is a faith position. You can't suggest that the absence of evidence is proof, even if there is a legitimate justification for lack of proof.

Hahahahaha! No, that's the "proof" that the intelligent designers use. I'm sorry that you were unable to notice that what I'm saying in this sentence is to absolutely agree with you: lack of evidence in the fossil record provides no proof that there was no expression of "junk DNA" traits.

 

Now the fact is that we can see such effects in real time today: there are oodles of papers out there that talk about it and it would be worth your while to Google it! :)

 

What makes your argument absurd though is that we're now seeing this huge library of potential for dramatic change in species sitting there in organisms that have been very stable but who also have not had the evolutionary pressures needed to cause a change. While we may have not figured out exactly the mechanism here it's incredibly silly to say that there's no way that functional "currently unexpressed" (it's not "never ever expressed") has nothing to do with PE.

Perhaps I should suggest that we have not demonstrated that they were expressed. And the timeframe (particularly for the Cambrian explosion) remains problematic in any circumstance. Further, the reduction in phyla in the last 500 million years does not fit very well with this framework either.

Well, purely from a standpoint of how complex systems work, I can tell you from my own experiences with learning systems that as they become more complex, radical divergence requires extreme changes in inputs and feedback loops (i.e. the environment). The Cambrian explosion occurred at a time where life was transitioning from very simple to very complex and lots and lots of different forms evolved out of the simple systems: there wasn't a whole lot of "previously expressed" templates to work with nor the mechanisms to suppress "bad ones", so lots of stuff got tried and lots of stuff developed, and it evolved rather rapidly in an environment what was filled with competing organisms and rapidly changing conditions.

 

As systems become more complex, they tend to follow the dictum "stick with what you know" *unless* there are severe changes to the environment, which cause such systems to start throwing out what they know and disabling protection mechanisms to try to survive: the Paleocene which was a pretty rich explosion, albeit much less earthshaking than the Cambrian *precisely* because the more complex systems tend to converge, so the "reduction in phyla" you complain about is actually well explained.

 

So:

 

So really, no, it's not that the were never ever expressed at any time, it's that they were recessive and not visible in the greater population UNTIL an environmental change caused it to become dominant in the population.

I do understand the position. But we have things that we know:

1. Recessive genes are more likely to express in smaller populations (by arithmetic)
   
2. The Cambrian explosion (and a couple others) occurred pretty quickly. We also don't have the advantage of large offspring count or frequent regeneration cycles once we get to higher phyla. It is difficult to advance a dozen phyla or two in 250 million years.
   
3. We cannot demonstrate that the recessive genes were ever expressed. It is OK to assume it, but it is certainly an assumption.
   
4. Speciation and phylogenation seems to have slowed down in the last 500 million years. Even if high phyla slowed due to smaller offspring count and rarer breeding cycles, there is no reason that lower phyla could not have continued to "climb the tree". This just does not fit the framework well.

Yes, we have things that we know:

1. Recessive genes are indeed more likely to express in smaller populations, which occur because of changes in environment and such changes are definitionally the punctuations.
   
2. The Cambrian explosion occurred because of dramatic changes in the environment (making it more conducive to life), along with relatively simple--and therefore mutationally uninhibited--organisms hitting an inflection point in productivity in evolving multi-cellular organisms. And with this mutational inhibition relatively undeveloped it is not difficult at all to advance a dozen phyla or two in 250 million years. Conditions so optimal for life that existed in the Cambrian emphasized evolutionary advancement as the primary success factor.
   
3. We may not be able to demonstrate that the recessive genes were expressed during the Cambrian, but we sure can now with existing species. Insisting in the face of that clear and observable evidence that it's merely an assumption that it happened then is like insisting that although we see objects fall to earth now, we can't *prove* that Newton ever observed anything fall, which is pure, unbridled Know-Nothingism.
   
4. Speciation and phylogenation seems to have slowed down in the last 500 million years precisely because that's what systems do as they grow more complex. Note the operative verb here "slow": not stop and not monotonically slow (see reference to the Paleocene above). And this actually has nothing to do with smaller offspring count and rarer breeding cycles (which if they really were dominant, would indeed cause monotonic slowing which we don't see). As to why lower phyla don't continue to "climb the tree," that is quite clearly due to the increase in competition along with the increased influence of mRNA inhibitors. Even when we get city sized meteorite collisions, we don't get the effect of the Cambrian, because that's a once in a planetary evolution event!

 

So, no the things that we know really don't cause the problems you claim and to promote them really is to promote ignorance of the last 50 years of evolutionary biology.

 

Moreover the point you've avoided so far is that environmental changes that make recessive genes dominant result in feedback loops that encourage cascade changes in what is expressed, either unleashing co-located genes or encouraging related genes that in combination become environmental advantages. That cascading is what makes it all Punctuated.

The more complex the cascade, the less likely.

That's actually categorically false: It shows up in AI and complexity theory all the time. In evolution there are oodles of examples: You get wings you can inefficiently fly. You get feathers you get wind protection and as an odd side effect less wind resistance, put wings and feathers together and you get a huge evolutionary advantage that--oh my goodness--results in a whole new phyla....

 

Unfortunately on this topic, there's almost no convincing the unconvinced because effects like I have described are not intuitive and are not commonly subjects of direct experience. AI is an amazing area of research precisely because of it's tantalizing similarity to natural systems of all kinds, not just intelligence. If you're not predisposed to looking for anything other than "it's all random or it's all directed by a supernatural being" it's hard to see all the real-world, naturally occurring analogs that are all over the place if you only look.

I am not sure who you are addressing here. I don't fall into either camp.

Oh I've been on the business end of your insistence that you're only trying to hold to a strict interpretation of the scientific method here, but the fact is you really spend all of your time defending--now easily--disproven arguments and never show any evidence that you've investigated them, evidenced here by the fact that you're defending Dembski's silly math--albeit using the cover of saying that it "poses issues that should be addressed". At the same time, you don't mention any recent research that does indeed address it quite handily, to the point where it looks like you're clearly avoiding it.

 

I tend to give Qdogsman and greylorn the benefit of the doubt about their real qualifications or understanding of the modern biology, but geewhiz, this is your job to know this stuff, and what you're doing here is tantamount to me ignoring the last 30 years of computer science and insisting that the only real applications should be built using COBOL on an IBM360. You know better than that.

 

I know you have your Bio's "Biological Big Bang" theory of front-loading everything (so "not meddlesome intelligence" just "front-loaded design" for those of you watching this), but that does run afoul of easily reproducible Shannon/Kolmogorov analysis. You might want to try that.

 

Now to finish this off on a positive note, I'd like to point you to a resource for your further edification on what I'm talking about. While there is an avalanche of information on the Internet on all the stuff I'm talking about here, one of the latest areas of research that is the basis for what I've described about how unexpressed sequences change and evolve now has it's own journal/website, mobilednajournal.com. One paper from 2009 has this to say about the topic (it's really quite readable, and I recommend that everybody read the whole thing):

 

Our ability to think fruitfully about the evolutionary process has greatly expanded, thanks to studies of mobile DNA. Laboratory studies of plasmids, transposons, retrotransposons, NHEJ systems, reverse transcription, antigenic variation in prokaryotic and eukaryotic pathogens, lymphocyte rearrangements and genome reorganization in ciliated protozoa have all made it possible to provide mechanistic explanations for events documented in the historical DNA record [6]. We know that processes similar to those we document in our experiments have been major contributors to genome change in evolution. Using our knowledge of genome restructuring mechanisms, we can generate precise models to account for many duplications, amplifications, dispersals and rearrangements observed at both the genomic and proteomic levels.

 

The genome DNA record also bears witness to sudden changes that affect multiple characters at once: horizontal transfer of large DNA segments, cell fusions and WGDs. These data are not readily compatible with earlier gradualist views on the nature of evolutionary variation. However, we are now able to apply the results of findings on the regulation of natural genetic engineering functions in the laboratory and in the field to make sense of the DNA record. Cell fusions and WGDs are events we know to activate DNA restructuring functions (Tables 3 and 4). Thus, it is not surprising that bursts of intracellular horizontal transfer, genome reduction and genome rearrangement follow these initial abrupt changes in the cell's DNA. How a newly symbiotic cell or one with a newly doubled genome manages the transition to a stable genome structure that replicates and transfers reliably at cell division is another important subject for future research. The lessons we learn about silencing mobile DNA by internal deletion [12] and RNA-directed chromatin modification [167] are likely to prove helpful starting points.

 

Although there remain many gaps in our knowledge, we are now in a position to outline a distinctively 21st century scenario for evolutionary change. The scenario includes the following elements:

 

1. hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering;
   
2. major disruptions of an organism's ecology trigger cell and genome restructuring. The ecological disruptions can act directly, through stress on individuals, or indirectly, through changes in the biota that favour unusual interactions between individuals (cell fusions, interspecific hybridizations). Triggering events continue until a new ecology has emerged that is filled with organisms capable of utilizing the available resources;
   
3. ecologically-triggered cell and genome restructurings produce organisms which, at some frequency, will possess novel adaptive features that suit the altered environment. Novel adaptive features can be complex from the beginning because they result from processes that operate on pre-existing functional systems, whose components can be amplified and rearranged in new combinations. Competition for resources (purifying selection) serves to eliminate those novel system architectures that are not functional in the new ecology;
   
4. once ecological stability has been achieved, natural genetic engineering functions are silenced, the tempo of innovation abates, and microevolution can occur to fine-tune recent evolutionary inventions through successions of minor changes.
   

 

This 21st century scenario assumes a major role for the kind of cellular sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel Prize address [1]. Such a cognitive component is absent from conventional evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgeable about cellular response and control networks. This 21st century view of evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions. It also answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties. In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science.

This is really, really fascinating stuff, and to ignore it is a crime!

 

I don't think Carl was discounting that either, but sometimes folks make it darn hard to appreciate them!

Well, I appreciate you.

Thank you!

 

I appreciate you tremendously too when you're not obliquely promoting ignorance! :cheer:

 

 

In science, fact can only mean confirmed to such a degree that it would be perverse to withhold provisional assent. I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms, :phones:

Buffy

[Biochemist]

I did! In the other thread you posted to dear! Anyways, Hiya Bio!

I saw that eventually. Nice to be back for a bit.

 

As you're a Biochemist, I know you've had the statistical education to understand dependent variables and the effect of Bayes Theorem on probabilities. If you don't, I hope to God that I've never bought any of your company's products.

Actually, I am probably a little bit more this direction than you are. More on that below.

 

...both Bayes as well as Information Entropy (Shannon) and Information Complexity (Kolmogorov) prove the opposite of what they actually show, which is that the information in DNA is highly correlated and interdependent.

Agreed. Although I don't know Shannon and Kolmo.

 

If every base pair in every sequence in every strand of DNA were "independent" none of the mechanisms you do believe in would work. DNA wouldn't actually instantiate morphology, scavenger DNA wouldn't know what to zap, proteins wouldn't know how to support replication, all because nothing would have anything to do with anything else.

.

I think we are still in the pretending-to-understand-this phase on this particular topic (Ubiquitin tagging). This tagging system is 1) incredibly complex, and 2) incredibly efficient. Nothing "foreign" gets past it. It is a bit of a stretch to suggest that all of the "genetic engineering" you discuss below would automatically be recognized as native protein. But it is. Hmmm.

 

Now as it turns out, that's exactly why Shannon and Kolmogorov have come into play......

I plan to look into this. Looks interesting.

 

It's pretty amazing to watch. But at any rate, if you're going to insist that there's a "probability problem" you need to catch up with the times: you sound SO last millennium, dear.

My daughter says that too. Get in line.

 

As systems become more complex, they tend to follow the dictum "stick with what you know" *unless* there are severe changes to the environment, which cause such systems to start throwing out what they know and disabling protection mechanisms to try to survive: the Paleocene which was a pretty rich explosion, albeit much less earthshaking than the Cambrian *precisely* because the more complex systems tend to converge, so the "reduction in phyla" you complain about is actually well explained.

My antennae go up whenever we start personifying a chemical. I get the same feeling when we look at the quaternary behavior of DNA (how it exposes a very small portion of a chromosome so that it can allow access to tRNA.) This chemical is acting like it is thinking. I still feel like we are discussing the very, very simple actions of cells (e.g., replication) when the real sophistication is in the chemical behavior of macromolecules.

 

We may not be able to demonstrate that the recessive genes were expressed during the Cambrian, but we sure can now with existing species. Insisting in the face of that clear and observable evidence that it's merely an assumption that it happened then is like insisting that although we see objects fall to earth now, we can't *prove* that Newton ever observed anything fall, which is pure, unbridled Know-Nothingism.

I am afraid that I did not make my point well. My point is that we cannot rule out that unexpressed recessive genes existed.

 

Speciation and phylogenation seems to have slowed down in the last 500 million years precisely because that's what systems do as they grow more complex. Note the operative verb here "slow": not stop and not monotonically slow (see reference to the Paleocene above). And this actually has nothing to do with smaller offspring count and rarer breeding cycles (which if they really were dominant, would indeed cause monotonic slowing which we don't see). As to why lower phyla don't continue to "climb the tree," that is quite clearly due to the increase in competition along with the increased influence of mRNA inhibitors. Even when we get city sized meteorite collisions, we don't get the effect of the Cambrian, because that's a once in a planetary evolution event!

If you are suggesting that by "slowing", complex systems can lose half of their complexity, I find that odd. And the notion of an increased influence of mRNA inhibitors is in itself interesting. Why would the complex system begin to "favor" limitations on complexity? And isn't a bit of a stretch to suggest that loss of half of the phyla is consistent with an increase in competition now? Wouldn't we expect that the loss of most phyla would create substantial additional niche space?

 

So, no the things that we know really don't cause the problems you claim and to promote them really is to promote ignorance of the last 50 years of evolutionary biology.

Ouch

 

That's actually categorically false: It shows up in AI and complexity theory all the time. In evolution there are oodles of examples: You get wings you can inefficiently fly. You get feathers you get wind protection and as an odd side effect less wind resistance, put wings and feathers together and you get a huge evolutionary advantage that--oh my goodness--results in a whole new phyla....

I think you are personifying chemicals again, but I will let this slide. And I don't think you can use the issue we are disagreeing about as a proof case. The point you said was false was that longer cascades are not lower probability. You are saying that longer cascades are higher probability than shorter cascades?

 

I know you have your Bio's "Biological Big Bang" theory of front-loading everything (so "not meddlesome intelligence" just "front-loaded design" for those of you watching this), but that does run afoul of easily reproducible Shannon/Kolmogorov analysis. You might want to try that.

 

1) I am pretty impressed you can find a post of mine from 8 years ago

2) I have not read Shannon/Kolmo yet

3) I have some additional comments on that earlier post at the end here.

 

...one of the latest areas of research that is the basis for what I've described about how unexpressed sequences change and evolve now has it's own journal/website, mobilednajournal.com. One paper from 2009 has this to say about the topic (it's really quite readable, and I recommend that everybody read the whole thing):

It is a good link , and I agree with everything in the part your excerpted.

 

 

The part I wanted to add to my 8-year-old post above is that the level of good basic science work on abiogenesis has jumped in the last 20 years. I am not really sure when I noticed, but by about 2000, folks started looking at is en masse. My digestion of all of the work at the moment is that the arrival of nucleic acids from harsh environments is likely. And, oddly, not just nucleic acids generally, but the exact 5 that we use (G,C,A,T,U). Further, it looks like we can make the same arguments about the 20 amino acids. If it were not true, it is hard to explain how some life forms in the 3.5 billion years since the first cell did not pick up at least one more amino acid.

 

My default assumption is not just that life is likely, but that life based on our 5 nucleic acids and 20 amino acids is likely as long as the ecosystem is roughly like earth. That likelihood is based on the atomic chart. These 100 (ish) elements drive toward those 20 amino acids and 5 nucleic acids in an environment like earth. The additional conclusion is that other forms of life are highly unlikely, unless the ecosystem is significantly different.

 

The falsifiable hypothesis would be this: Other similar planets of adequate age (probably what Star Trekkies would call "class M") should not only have life, but have a life tree that is very similar to ours, and be based on the same 5 nucleic and 20 amino acids.

 

It would be nice to live long enough to uncover verification or refutation.

 

Bio

Edited June 4, 2013 by Biochemist

[Biochemist]

To all the Buffy admirers:

 

The only problem with chatting with her is that the individual responses get longer, and longer, and longer. I apologize if we are either monopolizing the thread or boring the sock off of others.

 

But it is nice to chat with you, Buff.

 

Bio

[ErlyRisa]

Show some respect, there is a diff b/w religion and Science, or just the hard work and research a person did (Charles Darwin)

 

let's not say "Darwinism" --> your turning it into a religion: Just b/c your religious doesn't mean everything else should be.

[pagetheoracle]

Blamski, sorry for the late rely but I've been away from the forum for ages. If the mind is an organizing principle, then yes it is still working on life. We see it in minerals, plants and animals. As energy there is no definition in molten lava but as it cools it takes form (becomes organized into minerals, liquids, gases): Some would argue this doesn't show intelligence and I couldn't agree more but as know life requires certain parameters to exist within and 'perhaps' this is programmed into existence, in the same way we would create terraforming on other planets deliberately i.e. matter cools down and differentiates itself into the various parts and elements we know of, then plants use this to create an atmosphere (not because they consciously want to but again because this is what they are programmed to do in the way of terraforming), followed by animals and a bipedal life-form (Though not necessarily, just a shape that allows the making of tools) that then invents space flight and starts this process off on other planets: Star Trek's 'Genesis Device.'I'm not saying this means there is a 'God' just that an organizing principle (closer to The Buddhists idea of mind) may exist to self-replicate its existence as we have seen various forms of life do on this planet already. I see a chain here and one that develops in a specific way. Maybe the idea of the universe being like a computer (self-replicating and autonomous), may not be an idea that should be so easily discounted.

[pagetheoracle]

To quote Asimov, who like Stephen Hawking, thought our only logical direction is to move off into space:-

 

"The Earth faces environmental problems right now that threaten the imminent destruction of civilization and the end of the planet as a liveable world. Humanity cannot afford to waste its financial and emotional resources on endless, meaningless quarrels between each group and all others. there must be a sense of globalism in which the world unites to solve the real problems that face all groups alike. There are no nations! There is only humanity. And if we don't come to understand that right soon, there will be no nations, because there will be no humanity. The saddest aspect of life right now is that science gathers knowledge faster than society gathers wisdom. I wish that I could say I was optimistic about the human race. I love us all, but we are so stupid and shortsighted that I wonder if we can lift our eyes to the world about us long enough not to commit suicide. It is change, continuing change, inevitable change, that is the dominant factor in society today. No sensible decision can be made any longer without taking into account not only the world as it is, but the world as it will be.... This, in turn, means that our statesmen, our businessmen, our everyman must take on a science fictional way of thinking. I discovered, to my amazement, that all through history there had been resistance ... and bitter, exaggerated, last-stitch resistance ... to every significant technological change that had taken place on earth. Usually the resistance came from those groups who stood to lose influence, status, money...as a result of the change. Although they never advanced this as their reason for resisting it. It was always the good of humanity that rested upon their hearts. Until now in world's history, whenever we've had a dark age, its been temporary and local. And other parts of the world have been doing fine. And eventually, they help you get out of the dark age. We are now facing a possible dark age which is going to be world-wide and permanent! That's not fun. That's a different thing. But once we have established many worlds, we can do whatever we want as long as we do it one world at a time. What is really amazing, and frustrating, is mankind's habit of refusing to see the obvious and inevitable until it is there, and then muttering about unforeseen catastrophes. Isn't it sad that you can tell people that the ozone layer is being depleted, the forests are being cut down, the deserts are advancing steadily, that the greenhouse effect will raise the sea level 200 feet, that overpopulation is choking us, that pollution is killing us, that nuclear war may destroy us - and they yawn and settle back for a comfortable nap. But tell them that the Martians are landing, and they scream and run. Humanity has the stars in its future, and that future is too important to be lost under the burden of juvenile folly and ignorant superstition. There is a single light of science, and to brighten it anywhere is to brighten it everywhere."

 

I hope this isn't considered too off-topic but as backing for my views about the evolution of life on a planet and where it goes when it has made a success of itself on one particular world.