April 11, 2007

Evolution's Credibility Problem (part 3)

(Part 3 in a 3 part series)


We cannot just magically say that a mutation happens to produce the code for a new protein. The mutation must happen somewhere. If it happens over the top of an existing gene, then you've lost your original gene. And no matter how impressive the new gene sequence is, if the old sequence was important you may have just killed your organism. This means that the new gene must either supersede unused gene material (assuming such a thing exists), appear within an appended section of DNA, or be an improvement in line with the gene it is replacing. All three reduce the odds of a good mutation's survival, and the latter constraint would limit the scope of novelty.

Additionally, the mutation must either create or be contained within its proper domain. This is where it gets too complicated to continue describing things in detail, but suffice it to say that a gene must have certain controlling sequences in place for it to be effectively translated. For instance, there are start and stop codons, which define the boundaries of the gene. Within this there are things like promoters and ribosomal binding sequences to be considered. And even the best gene instruction is useless unless it has the proper signal sequence defined at its start to act as a sort of mailing address so that the machinery of the cell can know where the resulting protein is to be shuttled and deployed.

So, a workable mutation not only must result in sensible coding for the protein, it must include all of the logistical elements as well. If it does not produce these or happen in a way to make use of those which exist, then it is worthless. Worse, the mutation could easily manage to overlap these controlling sequences in such a way that it not only destroys an existing gene, but also could damage a gene next door if the overlap crosses the domain boundary.

Another consideration is based on the stunning recent discovery that many genes actually overlap by frame shifting of nucleotides or by inverse coding (up to 6 possible genes could be theoretically coded in the same physical space). This means that a change to even one nucleotide in the overlapping region could damage more than one gene. Risking damage to such a code base is one thing, but producing such a thing in the first place is a whole new dimension of incredible. To come close to understanding what I mean, simply imagine creating a palindrome more than 100 letters long (which is grammatically correct), even by design! Evolutionists would have us believe that this has happened countless times by mere chance.

Something else that I would point out: when we are dealing with creatures that sexually reproduce, a favorable mutation in one of the many cells of the organism (e.g., humans have trillions) is meaningless in evolutionary terms. This is because only germ cells are passed on to the next generation. Only mutations that happen in the few eggs or sperm that result in offspring are even candidates for evolution's "descent and natural selection." This means that the higher-order creatures that sexually reproduce, have fewer offspring, and longer generation cycle times, should theoretically evolve slower. But guess what: the quiet reign of single-cell organisms, which exist in vast quantities and reproduce fast and furiously, supposedly lasted more than 2 billion years; whereas the entire history of the relatively slower, fewer, and more diverse plant and animal kingdoms has occupied only a quarter of that time. And humans, some of the slowest breeders of all, appeared in a geological flash.

But back to my lactose-handling enzyme. Even this conceptually simple protein adaptation is far more complex than I suggest. In reality, beta-galactosidase consists of 1023 amino acids and actually functions in a larger structure composed of 4 of these proteins fit together. There are very few simple jobs in the cell. The protein "machines" to do the work are often quite complex, sometimes involving numerous independently designed proteins working in cooperation where the absence or poor design of even one would completely cripple the entire machine. And the machines generally require separate helper and regulating proteins to allow them to either do any work at all or to suppress them when they are not needed.

In the case of the relatively simple beta-galactosidase, it needs at least two other proteins: a permease that permits lactose entry into the cell (not just any 'ole thing is allowed in or out), and a repressor that works to inhibit the production of beta-galactosidase when there is no lactose in the neighborhood (there's no advantage in wasting precious resources). To further complicate things, each of these three components is found in the DNA in sequential order and is packaged together as a single unit, called an "operon."

Aspects of the cell are much like a factory, and just like in a real factory no single machine does much work in isolation. For example, in the case of the bacterial flagellum, a microscopic rotary motor, there are over 40 unique proteins that are involved in its architecture, and many more that are involved in its assembly and operation. As complex as individual proteins may be, establishing their place in the economy of the cell adds greatly to this complexity and cannot be overlooked. All of biology is characterized by interdependent systems — it is the norm.

In summary, the "small," incremental steps proposed by evolutionary theorists are astonishingly non-trivial and, in practice, can be as interdependent at the molecular level as a bat's various features are at the higher morphological level. What I describe is only the beginning of the many incredible things in the world of biology that evolution claims to explain. The more we learn and the more deeply we look at nature — into the microscopic world that Darwin could not have imagined — the more numerous and profound the required work of evolution seems to become. As I've said elsewhere, "Evolution gives fat chance a full time job."

Is there no room, then, for grace toward those who are unconvinced by the evolutionary story? Skeptics should be able to reserve the right to exercise the same principle of credulity that evolutionists themselves apply elsewhere. There is no denying that circumstantial evidence exists for the theory, but the explanatory work that evolutionists are seeking to do with it needs a mighty big engine to push this load over the hill of plausibility. And the fact that the theory itself is immune to reconsideration, in spite of the constantly pounding waves of unexpected and complex new biological discoveries, only fuels suspicion that there is something more than objective science behind it.

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14 Comments:

At 4/13/2007 9:16 PM, Blogger Psiomniac said...

Except that it isn't chance. It is a racheting system of cumulative change that has had Deep Time in which to operate. I'm afraid your post amounts to an Argument From Personal Incredulity.
You look at the staggering complexity of the cell and yet wonder why it took so much time to get beyond the single cell stage. The answer is staring you in the face.

 
At 4/14/2007 10:05 AM, Blogger Paul said...

But each of the changes which are said to have accumulated are a matter of sheer chance at every step -- random mutations are the driver of it all. I readily admit that if a beneficial mutation were introduced into the population, then natural selection may well take hold of it and carry it forward into subsequent generations (though there are some noteworthy problems of genetic dilution to overcome).

The problem relates to the probability of achieving each one of these remarkable mutations, which would have to number in the billions to yield each of those things staring you in the face at the zoo. Your time is not "deep" enough unless you can find some statistical loophole to the problem of generating individual, beneficial mutations, much less the countless cascade of them required to do the necessarily work. In my experience, these statistical problems are merely shrugged aside by evolutionists and they simply excrete the kind of optimism that you express.

Regarding personal incredulity, you are right that just because something is hard to believe does not mean that it didn't actually happen. However, as I've carefully argued in this series, credulity is a practice we all apply where the processes and probabilities are insufficient for the task. For example, if I told you that I had swum from the US to the UK you would surely think that claim lacked credibility. Does the flawed Argument from Personal Incredulity negate your unbelief? Certainly not, because you have reason to believe that such a thing is problematic on many levels. That is what I am claiming about evolution: that it is dependent upon a host of absurdly improbable events. You'll have to demonstrate that they are either factual or at least probable in order to call my incredulity into question.

Your last two sentences are not helpful. I think you may be referring to the incidental comment I made regarding the relatively short history of sexually reproducing organisms vs. the long reign of single celled ones. But here I was not remarking that it took so long to get to this more complex stage of life; I was remarking that the vast diversity and progress supposedly made in this later stage of evolution was done in both a shorter period and with longer generation times. For instance, in the average lifetime of a human a bacterium like E. coli can go through up to 600,000 generations of growth. That's the equivalent of 12 million years of human reproduction. By comparison, this makes all of the vast post-Cambrian development happen in a snowball-rolling geological flash.

 
At 4/15/2007 2:56 PM, Blogger Psiomniac said...

I take your point about swimming the Atlantic and incredulity. I suppose when the people who do analysis of transatlantic journeys for a living tell me that people have come across on flying vehicles (though they might not be able to give me an engineering spec) I think their view is more sensible than amateur conspiracy theorists who say that the experts are in league and in fact it is all done with flying carpets.
I'm sorry you did not find the last two sentences helpful but I think that they address the fact that the point you are making regarding the different amounts of evolutioary timescales is not valid. It might take a billion years or so to build the complex cellular machinary for single celled organisms. But greater progress and diversity can only take place once some design tricks have been 'discovered'. For a start, the ability of cells to join together to form multicellular organisms. There are also questions about how you would measure 'progress' or 'diversity'.

If you think time is not Deep enough then your model of how mutations are incorporated into evolutionary 'design' is too simple.

 
At 4/17/2007 7:19 PM, Blogger Paul said...

Psio,

It sounds to me like you are basically saying that since most "credible" scientists believe in evolution, then I am unwarranted in my skepticism of the theory, no matter how many issues I observe or might be able to demonstrate through personal knowledge of the actual science. Are you suggesting that I should simply believe a thing merely because it is imposed upon me by society and my "superiors?" This sounds like the kind of "faith" that religious people are accused of exercising. Do I not have a right to question orthodoxy and call for an accounting for the theory (to "think for myself")? Is science really this dogmatic and infallible?

One of the things that woke me from my own dogmatic slumber was the realization that I had never really even been presented with a reasonable proof for the theory. It was just asserted as fact, and anyone who questioned the theory was simply ridiculed into silence (I, myself, was guilty of that). There is an unusual emotional aura surrounding this theory like nothing else I've encountered in science. The only thing comparable was the big bang theory. That theory, like ID, was also once in the minority, just as evolution itself was. That theory also had great metaphysical implications, and many astronomers and physicists were candid enough to share their personal distaste for it.

But the implications of big bang theory are nothing compared to the implications of a failure of evolutionary theory. We may endlessly debate over what came "before" or "caused" the big bang, but if a "natural" process cannot be found to explain the origin of life, then what creation story is left to atheism? Like it or not, it is a non-negotiable for secularists -- indeed, as Dawkins said, it makes it possible for an atheist to be intellectually fulfilled -- and it has not escaped my attention that some of the most aggressive (I might even say "giddy") advocates for evolution, from its outset, have been committed atheists.

I know that ID, to a large degree, is advanced by committed theists, but there is certainly far more variety of opinion over this issue among theists, and they have found many allies among the deists and agnostics of the world. On the other hand, atheists, almost to a man, are in lock-step in their support of the theory. And those like Dawkins and Dennett seem to delight in using it as a "universal acid" to erode all "traditional" beliefs for which they are opposed. This is what reeks of "conspiracy" to me.

You said:
It might take a billion years or so to build the complex cellular machinery for single celled organisms. But greater progress and diversity can only take place once some design tricks have been 'discovered'. For a start, the ability of cells to join together to form multicellular organisms.

First, there were not billions of years available to build single celled organisms. They appear in the fossil record very shortly after the Late Heavy Bombardment period of the Hadean. There is good reason to believe that even after the cooling of the earth, there were numerous sterilizing events which occurred regularly almost right up until the time that evidence of life first appears. Life seems to appear in a flash, which means, at most, only millions of years to go through the various alleged phases of proto-cell to prokaryote evolution. And I will admit that, since it is so very complex, once you get to the cell you've got a lot of your work done. (There's an added twist here regarding eubacteria vs. archaebacteria -- they both appear early yet are so wildly different -- but I won't expound on this now).

Second, I will also admit that there would indeed be much more work to do in the single cell to get beyond its individualistic nature -- it would need to develop sister genomes and devise ways to communicate and activate/deactivate genes between siblings (much like a queen ant carries in herself the instructions for workers, soldiers, drones, etc). However, evolution doesn't work by discovering tricks that it can later employ when it's got its bag full -- it doesn't save up or plan. Each trick must provide direct and immediate benefit or it will tend to be lost by either selection or further mutations (which selection would allow, since they would occur in currently unused gene space). For this reason, there is no warrant for thinking that evolution in the single celled organisms would have batched up a collection of functions that would later bear rapid evolutionary fruit in the higher order creatures. Each gain in the higher order creatures would be its own unique lottery win.

And in the multi-cellular world, the organism now has to focus on gains and controlling mechanisms that affect each of the unique flavors that the cell can take. The diversity of the sister cells is all packed into the same DNA and there is much more to manage and coordinate (one reason why bacteria has less DNA). You know what they say: the more features on your car, the harder it is to service and the more that can go wrong. Problem is, now the cells (the germ cells that is) are doing all this even more complex work in smaller population groups and longer cycle times -- several orders of magnitude less opportunity for change.

Do you at least begin to appreciate the oppressive complexity of the task that evolution would face? And I am only touching on things that any first year biology students should know; there is far more complexity that I have not discussed and which is still being discovered. I have been exposed to materials from various pro-evolution biologists and they never fail to disappoint me in expressing their wonder over the "design" and "engineering" of it all. But even though they may admit their candid astonishment over their observations, they will still, with almost no explanation or statistical backing, ultimately wave their magic evolution wand over it to explain it all away.

 
At 4/25/2007 6:37 PM, Blogger Psiomniac said...

I am saying that although you are intelligent and the your grasp of the concepts is good, you don't do it for a living. The vast majority of those who do this for a living and have a track record of getting stuff done disagree with the conclusions you draw from the evidence. So do I. So it would not be rational for me to believe your view given that: a) neither of us are professional biologists, b) the vast majority of professional biologists disagree with you and provide arguments as to why and c) I find their arguments more convincing than yours.

Now, if evolution were credibly shown to have serious problems tomorrow, would that mean that the 'creator god with a personal interest in us' theory is the only other game in town? No.

As for your theories about when or whether life could have survived on the new earth and so called 'sterilising events', well if I came out with something like that you would label it 'speculation'.

 
At 4/25/2007 8:28 PM, Blogger ephphatha said...

psiomniac, I hope you don't mind be being persnickety. It could be that I just have a misunderstanding. I get the impression that since you aren't a professional biologist, you're not really qualified to judge the case for or against evolution. Instead, you take it on the authority of the experts.

But if that's the case, then you must be saying you aren't really qualified to say whether or not Paul's arguments are sound. Otherwise, why point out that you're not a professional biologist?

But then at the end, you said you found the arguments of the professional biologists more convincing than Paul's. That seems to imply that you ARE qualified to assess the soundness of the arguments. But if you're qualified to assess the soundness of the arguments, then why point out that you're not a professional biologist?

Do you see what I'm asking? I'm not sure if I'm being clear or not.

Besides natural evolution and some kind of intelligent designer, what other options do you think are in town?

 
At 4/26/2007 4:20 AM, Blogger Psiomniac said...

ephphatha,
I don't mind at all.
First, we all defer to experts in fields that are not our own. How could it be otherwise? We still have to assess the arguments presented by the experts though. Clearly there is an interface problem in that there are necessary simplifications that must be done to present complex findings. However, we can look at the methodology of the work, check its peer review credibility and if it is really important, study and gain some expertise ourselves.

You said:
"But if that's the case, then you must be saying you aren't really qualified to say whether or not Paul's arguments are sound."
Paul (as far as I know) is not a biologist and as such his arguments are not technical to the degree that actual biological research is. His conclusions are more like statements of incredulity about the efficacy of the proposed mechanisms of evolution, given the complexity of biological systems that he has sketched. I have read the arguments of professional biologists that have addressed these points and have found them to be persuasive. There is no contradiction here.
I think that Paul is as qualified as I am to assess the presentation of evolution to the lay audience by biologists. I don't agree with his assessment. So there is a distinction between assessing Paul's arguments (and also lay targeted arguments presented by biologists) on the one hand, and directly assessing biological research itself. The latter would be peer review, which I am not qualified to do.
In this context, quite apart from the independent fact that I find the arguments of biologists more persuasive than Paul's, it is rational for me to ascribe more weight to what biologists say than to what Paul says.

 
At 4/26/2007 4:27 AM, Blogger Psiomniac said...

Sorry, I forgot to address your last point. You asked what other options are in town. Well, I won't detail the few I could think of off the cuff because I feel that this would be counter productive. Suffice to say the possibilities are legion.
If evolution were completely undermined tomorrow we would be left scratching our heads and being forced to admit that the only reason that some might prefer a benevolent creator god over space ants as an explanation for the origin of life is a cultural/psychological reason rather than a rigorous assessment of the evidence.

 
At 4/26/2007 6:46 AM, Blogger ephphatha said...

psiomniac, whether you're talking about a benevolent God or alien creator ants, in both cases, you're talking about some kind of intelligent designer, right? What I'm asking is besides natural evolution and some kind of intelligent design, what other options are in town? I'm just curious to know there's even ONE other option, because I can't even imagine one.

 
At 4/28/2007 11:15 AM, Blogger Paul said...

Psio,

"I am saying that although you are intelligent and the your grasp of the concepts is good, you don't do it for a living. The vast majority of those who do this for a living and have a track record of getting stuff done disagree with the conclusions you draw from the evidence."

All I can say is that this is too important to simply accept on consensus. Every scientific fact was once a minority position, and every wrong theory has seen its own heyday. This theory has far too much philosophical baggage attached to imagine that I can just blindly accept the assertions of a largely secular academy and fawning media.

My own knowledge is obtained at the hands of supporters of evolution, so I don't think my understanding negligent. And I've recently been seeking to get up to speed on the latest findings in cellular biology (such as just what it is that is being discovered in that "Junk DNA").

Ultimately, I must make my own belief decisions, and for someone like yourself, not inclined to allow design a foot in the door, I can only give food for thought. PhD's in these matters have said more than I, but it would seem that you must reject them because, however credentialed they may be beyond the average scientist, they are simply in the minority (or perhaps have a theistic "bias").

Personally, the more I learn, the more nature screams design and insane improbability at every turn. Increase in knowledge does not reduce the complexity to be explained or give any aid to statistical probabilities. If I have misread my facts, then I welcome correction; or perhaps it can be demonstrated that functional proteins can occur in only a few orders of magnitude less arrangements than the number of all possible combinations; otherwise, you are free to stand upon your materialistic optimism and your majority report and we will simply have to agree to differ once again.

"Now, if evolution were credibly shown to have serious problems tomorrow, would that mean that the 'creator god with a personal interest in us' theory is the only other game in town? No."

First, I will share that my next post will deal with something very much like this question. Second, I must agree with Sam that it's either intelligent design of some sort, or it's a natural process of some sort. The "evolution" label would surely survive any reworking of that natural process, as it already has.

As far as who that "designer" might be, you are right that it could be, in theory, a non-divine entity, but I can offer reasons why this is not likely. Another point I often make is that according to the present constraints put upon ID we would never discover that we had alien designers, since natural processes seem to be the only allowable solution or peer reviewable idea. Additionally, if the designer were deity, then it is not such a stretch to think that the one who designed us did so out of "personal interest." It is a deity who simply spews out a universe to see what develops (implying theistic evolution) who might best be accused of indifference, but that is not what I propose on either theological or scientific grounds.

"As for your theories about when or whether life could have survived on the new earth and so called 'sterilising events', well if I came out with something like that you would label it 'speculation'."

I'm not speculating; I'm simply following the majority report on this (which looks to me to be well founded).

As the story goes, first life (complex cellular) appeared unquestionably at 3.5 billion years, and earlier than 3.8 billion by many accounts. Earth's formation was complete around 4.5 billion years ago, which leaves less than 1 billion years, at the longest, for chance to work its magic. However, this stretch of history is known as the "Hadean" for a reason (named after "Hades").

After main planetary formation there was a period of planetesimal bombardment that tapered off by 3.8 billion years (there was actually a rise in frequency shortly before that time: the "Late Heavy Bombardment"). Some of these were continent sized, and, in fact, the present theory of moon formation has a body the size of Mars striking the earth at some point after its formation. The age and volume of craters on the moon attest to the bombardment that occurred after moon formation — Earth being more massive and thus getting the brunt of the collisions.

So, to say that at least a handful of these impacts were sterilizing is not unfounded speculation on my part. Here is a rather balanced article to support my claim. It offers hope that things were not as hellish as once believed, while still admitting to some sterilizing events. All this serves to squeeze the window in which life could have existed upon earth, much less progressed through its many required "protocellular" stages of development to arrive at something as complex as cyanobacteria.

 
At 5/01/2007 9:37 AM, Blogger Psiomniac said...

ephphatha,
I never said the Space Ants were intelligent!

 
At 5/01/2007 9:57 AM, Blogger Psiomniac said...

All I can say is that this is too important to simply accept on consensus. Every scientific fact was once a minority position, and every wrong theory has seen its own heyday. This theory has far too much philosophical baggage attached to imagine that I can just blindly accept the assertions of a largely secular academy and fawning media.
Well, all I can say is that I am not blindly accepting anything, that every scientific model that has subsequently remained unfalsified has had its critics and dissenters, and of course we all have our baggage. I'm not convinced mine weighs more than yours though.

If I have misread my facts, then I welcome correction; or perhaps it can be demonstrated that functional proteins can occur in only a few orders of magnitude less arrangements than the number of all possible combinations; otherwise, you are free to stand upon your materialistic optimism and your majority report and we will simply have to agree to differ once again.
Like I said on another post, it is relatively easy to get the model wrong and point to the unfeasible nature of the result.

The "evolution" label would surely survive any reworking of that natural process, as it already has.

Perhaps, although how legitimate that would be might depend on the process.

On your next point, yes no doubt you can offer reasons why the designer is good and benevolent. I doubt that I would find them persuasive though.

On the sterilizing event hypothesis, it seems vague to me. Which events were sterilizing beyond reasonable doubt given we don't know how robust early replicators were, and what is the error bar on the date of their occurrance?

 
At 5/02/2007 11:49 AM, Blogger Paul said...

Psio,

"On your next point, yes no doubt you can offer reasons why the designer is good and benevolent. I doubt that I would find them persuasive though."

You misunderstood me. I said that I could offer reasons why it is not likely that the "designer" was non-divine, i.e., it was not space ants or other parties within nature. I'll save the "benevolent" idea for another discussion.

"On the sterilizing event hypothesis, it seems vague to me. Which events were sterilizing beyond reasonable doubt given we don't know how robust early replicators were, and what is the error bar on the date of their occurrence?"

I don't think it's unreasonable to suppose, as many do, that at least one of the impacts in the late bombardment period stirred up enough magma to sterilize everything (thermophiles like it hot, but not that hot). And the collision event resulting in the moon mixed up enough material that even the core of the incoming planet was transferred to the Earth.

However, I'm certain that I will not crush your optimism, since you very much need that extra time prior to 3.8 Ga to do all the necessary work in getting full-blown bacteria by then. I might mention that there seems to be evidence for both Eubacteria and Archaebacteria in the early record -- the latter being the extremophilic kind (heat/cold/acid/alkaline loving) that you are putting your hopes in.

I may be blogging on some of the issues surrounding the cellular classifications, but in preview I will share that these two types of organisms, while sharing some common structural features, are radically different, both genetically and compositionally, e.g., their cell walls and other structures are made of different materials, and their gene transcription and protein expression is different. In fact, by many measures they are as far apart from each other as the Eukaryotic cells (which make up plants and animals) are from Eubacteria. There are even reasons to consider the Archaea to be more closely related to the Eukaryotes, which didn't appear on the scene for another billion and a half or so years.

All this means that you have two distinct groups appearing very early on which require a great deal of prior evolutionary history to get to some common ancestor, much less back to the many proto-cellular intermediate stages. In any event, you do not have "billions" of years of biochemical broths to stew up something interesting (assuming such soups were even available). The work of abiogenesis and the evolution of the Prokaryotes would have to proceed at a relatively brisk pace, even if it had an undisturbed time span from 4.5 Ga to 3.8 Ga to do so.

Regarding your "robust early replicators," it is true that many of the Archaebacteria are capable of living in hostile conditions. However, being able to live there and being able to arise there are two different things! The same heat and/or toxic conditions in which some Archaeon thrive would serve to destroy most of the molecules of which they are composed. It is the integrated whole which works in concert to keep these organisms alive, but in evolving such organisms you must first generate an abundant supply of the parts upon which the whole may progressively be assembled. To think otherwise would be like claiming that because a tank can survive battlefield conditions, then it follows that it could have been assembled under heavy enemy fire.

 
At 5/03/2007 7:01 PM, Blogger Psiomniac said...

Good parting analogy there, I like that.
It seems to me that you are trying very hard to package speculation about the nature of early replicators and about early bombardment as authoritative whilst at the same time implying that the pessimistic time span is not enough to give life a chance-almost as if you had a way of calculating this that we could inspect.

 

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