Increasing Genome Information (Part Two): Conjugation

[AfterFauve001]

Sadly I hear more of the fundamentalist nonsense from science videos.

this is great science don't pollute it with garbage - I almost clicked off these videos when you started mentioning creationism.

[PhxPride1]

evolution exists, God exists, and I'm thankful that you exist and posted this video! thanks pal!

[IMBLUESTREAK23]

This was a fantastic video until the final 20 seconds. The attack on "fundamentalists" or those with religious affiliations was extremely uncalled for. 1/5

[massspectrician]

I made this video specifically to address an argument that I've heard countless times in the fundamentalist critique of the Theory of Evolution. I have posted this video specifically to address a mechanism by which genetic information can increase to counter that tired and flawed argument. As such, the "attack" was certainly "called for".

[t0xyg3n]

the entire video is debunking a fundy argument against evolution. this argument isn't posed on any scientific grounds, but solely because the science has shown their beliefs to be false.

it was warranted

5/5

[tubewatch59]

In summary, I devastate all opposing viewpoints with the following certainhoods!

1. I.D. is nice.

2. Evolution is no solution!

3. I'm Dembski's lapdog: ('woof')

4. Heh heh, it's Behe!

OK?

[tubewatch59]

These processes are in effect for bacteria. But it does look like an intentional designed process to network the information in bacteria. On the other hand it seems that this process is not in effect in higher life-forms. So even though bacteria do indeed increase their information, it seems to be a process of adding existing information modules. And it's not a general process extending to higher life-forms. It's more of a specific, limited process, than a fundamental process of all evolution.

[tubewatch59]

I'm not saying you didn't answer your critic. I'm trying to imply that this process is too well regulated (like much everything else inside cells) to be a naturally occuring mechanism. It would require a great deal of existing machinery to function in the first place and thus leaves a large gap in the naturalistic origin of bacteria and also the higher organisms. It is a much more sophisticated mechanism than gene duplication which seems to be a haphazard nonregulated process.

[tubewatch59]

Gene duplication itself is also subject to removal by natural selection quite quickly due to the effect that the duplicated gene's dead weight has on the organsisms with it. They take longer to reproduce. It has been shown that these extra gene copies get truncated away before they have enough time to accumulate enough mutations to realize additional novel functions. I know evolution is real, but it's more of a degenerative process leading to niche adaption at the expense of overall viability.

[massspectrician]

'Gene duplication itself is also subject to removal by natural selection'

What crap. I shouldn't have to point this out but here it is ... YOU HAVE AN EXTRA COPY OF YOUR ENTIRE GENOME! Redundancies are actually good things as they act as back ups for genes and which hedge against deleterious mutations in required genes.

'Evolution is ... more of a degenerative process'.

Precisely the position I am crippling with these videos.

[tubewatch59]

"YOU HAVE AN EXTRA COPY OF YOUR ENTIRE GENOME!"

No. And extra genes are dead weight until they can provide whatever you think they can be used for. Natural selection will delete them on average long before they could theoretically evolve any beneficial mutations. It's a fanboy fantasy! If there's a choice between an efficient genome or one lugging around another gene then the one that gets 'better mileage' is going to win. The other will be evolved away.

[massspectrician]

Yes, you are a diploid and therefore have two copies of every gene in your entire genome. I don't see how you can still push this. Are you denying that you are a diploid? Seriously, do you know anything about the human genome at all? This ad hoc argument would lead one to the conclusion that humans (along with most other animals and plants) shouldn't exist.

[tubewatch59]

Diploidy! Well sort of, but it isn't a true copy. (I thought you meant the other DNA strand). It isn't carrying a truly redundant copy of the genome. It's similar but different, providing variation. Like plasmids etc., it's setup that way. There's also the question: Why is it there? Evolution should have deleted it, if not for the fact it was already set up. It's redundant in concept perhaps, but not in operation. Gene duplicates are redundant, so get deleted.

[massspectrician]

Again, your statement is false. Having extra copies of genes is often results in positive selection. You are cherry-picking through evidence. As far as addressing 'Why is it there?' I will but you will have to be patient. I am working on my next video presently and will likely be dealing with prokaryotes for at least 3 more presentations. Then I will start talking about the origins of eukaryotes and then I will get into gene/chromosome duplications. Be patient and I will address this.

[massspectrician]

Ok, so having two copies of your genome PROVIDES VARIATION. Precisely what I am saying. Genetic diversity is a good thing for which evolution conserves the duplication, not deletes it. Saying otherwise is a either naive or a lie.

[massspectrician]

This is the argument people use known as 'irreducible complexity' and it has failed over and over and over. What qualifies a process as 'too well regulated ... to be naturally occuring [sic]'? Remember when Micheal Behe said that about the bacterial flagellum and Ken Miller totally pwnd him in court? This statement is completely contrived and disingenuous. Intelligent Design is nothing more than a poorly-guised string of ad hoc reasonings toeing the creationist line.

[tubewatch59]

Ken Miller is putting up the notion that any other possible functions for any sub-components will 'pwn' I.C. No. You ought to know better! You and Ken are forced to conclude that some kind of a chain of intermediate functions not related to the final function will evolve and somehow happen across the fully setup I.C. system. If you weren't committed to evolution you would be laughing your head off at such an absurdity. But faith can do amazing things. Enjoy!

[massspectrician]

Your denial of your own diploidy shows how incredibly weak your understanding of genetics and evolutionary process really is. You just have faith you are right, that is it. Unfortunately, empirical evidence that discredits your claims doesn't seem to have any effect on you. The term irreducibly complex infers that the system would be useless without all its parts, this was shown to be false. Once the machinery is in place, novel functions can develop.

[tubewatch59]

I thought you meant the other strand. And you know more than I do, sure.

"The term irreducibly complex infers that the system would be useless without all its parts, this was shown to be false."

Nobody gets this right! It is useless in terms of the original function. Once the irreducible core components are deleted, the system won't function as what it used to be. The 'gradual evolution' is gone. That's why the sudden appearance of novel integrated functions is absurd in I.C. machines.

[massspectrician]

You are working backwards with this logic. If you have component parts that give a function to an organism that is positively selected for, conservation of the genes that make that process work will be conserved. We can look at all 'irreducibly complex' systems and determine whether or not the component parts are useful, through comparative protein sequencing. If the component parts are useful, then they will be conserved and a more complex function may evolve as more components are acquired.

[tubewatch59]

The protein components of a molecular machine are always going to be useful. Homology suggests evolution as one explanation. However it also suggests the design notion that useful proteins are re-used to build different things. Only the design explanation overcomes the difficulty of putting an I.C machine together. There is no continuity of function. The roles are going to alter. How, really, is that going to be achieved? It's exceedingly unlikely to hit on working versions of novel machines.

[massspectrician]

Again you refer to probability? Show me your math!

[tubewatch59]

Obviously I am not an expert on this. What I will say is that all complex functional systems have the characteristic of following a highly inhibited set of motions and arrangements in order to carry out their function. It's not that they have immense freedom of motion, its more that they have highly specific motion and signalling and timing. In a large complex system this implies that the large numbers of degrees of freedom require that the workable configuration is a tiny subset of the ...

[tubewatch59]

... possible arrangements that could have existed. In other words the working configurations are always 'needles in a haystack' compared to the vast number of non functional, or even, functional but not specifically advantageous for the particular requirements neccessary.

Given the flagellum, a reasonable number of working variations that perform well could exist. Then there would be far more variations that perform, but poorly. Then vastly more that almost work but are disabled in some ...

[tubewatch59]

... some minor way. Then a whole lot more that retain the vague form of the flagellum but do not work at all. And then astronomically more that do manage to assemble into something, but do not resemble the flagellum and do not work, and then even more again, that do not assemble to form anything, or just many small blobs of useless material.

Now in all of those, there would be small functional elements that may even be simple enough to evolve. But their functions are not related to ...

[tubewatch59]

... any kind of motility function (in general).

It seems that we are being asked to believe that the evolution (or emergence) of these kinds of new functional elements are going to (over periods of time and vast numbers of trials and errors) arrange themselves into various working systems that will then over more time, change and eventually work their way up to arranging themselves into a system like the flagellum, which of course isn't an end point, just a transition to some other system...

[tubewatch59]

But the problem is that each of these 'functioning systems' is like, highly isolated from other possible functioning systems. You can tolerate variations within a system, some of which are beneficial, some of which are neutral and some of which are harmful. It is naiive to imagine that there is a connected continuum of functional systems leading to ever more complex forms. This can only happen when the system in question has the special features of being non interdependant, or ...

[tubewatch59]

... interdependant in a loosely coupled way, so that variations or disabling of sub-components do not disable the whole system as the parts which make up the system are highly tolerant of this kind of change of component behaviour. That is what programmers try to achieve in object oriented program/computer architectures. They are fault tolerant. And obviously there are many such systems in life. I am not denying that. However in a great many systems such tolerance is not the case...

[tubewatch59]

It is the irreducibly complex machines that highlight this situation. Such machines DO have non essential parts, but if it's truly irreducible, then it is observed that a subset of the parts form an irreducible core of components. If any of those are disabled then the normal function ceases. There may even be other functions going on, but these modified functions are not the original function which has now been lost. Also, the usefulness of any possible remaining functions is doubtful...

[tubewatch59]

...The problem for evolution is that it has to find it's way from one set of functional groupings of components to another and somehow eventually get to what we now observe. If it's jumping (using mutation) from one set of functions to another, then there has to be a convergence of two functions existing. That's hardly ever the case. A new functional system that evolves will be conserved, it won't wildly vary off into non-functionality until it encounters the next working system...

[tubewatch59]

But say it's a gene copy therefore redundant, and assuming natural selection doesn't dump it to streamline the organism.

Theoretically, mutations are free to take place involving searching out non workable states until a functioning solution is hit upon, in which case it will be counted as a success. But what is the limitations of such a scenario? Because that is what I do believe can happen in some instances. Sometimes even in working genes a simple mutation can alter the function...

[tubewatch59]

But the point is, the functions are simple ones. Able to be evolved to fairly quickly. And with small numbers of mutations. And it's a local fitness peak that natural selection tries to preserve. And in the process, most of the time, the original working gene has now been modified to a new function but in general the new function is simpler than the original. That's why evolution is degenerative. It breaks things. Sometimes, just sometimes, the damage is useful. 1 step forwards, 6 steps back!

[tubewatch59]

Coming back to one of my original points. The evolved functions are 'small potatoes' compared to the big irreducibly complex functioning systems. Evolution can't get you there. The numbers are too big. The search takes too long because it's unable to be guided by natural selection. A random search with something the size and complexity and interdependencies of the flagellum utterly cannot happen according to this line of reasoning. Evolutionists of course will propose how it can happen...

[tubewatch59]

What is the flagellum in length of DNA? Something like 20000 DNA bases long or thereabouts. There is redundancy of protein coding. How much that is I don't know but assume that it's as high as an 80% tolerance to variation in DNA to give te same resulting protein (which I think is overly generous, but I'm no expert!) So that would reduce the 'length' of DNA to 20% of 20000 which is 4000 (nonredundant) length. The number of possible combinations are still 4^4000 ~ E+2400. That's big...

[tubewatch59]

Clearly, there would be many many many possible codings for a flagellum, so accounting for those would soak up a little of that number. But it's nuts to assume that you could reduce that number all the way back to something within the realms of chance and time (natural selection is sitting this one out) say down to 1E+50 or less. Clearly to me (I guess not to the majority of scientists) that figure of 10^2400 isn't going to be significantly whittled away. It strongly suggests intelligent design.

[massspectrician]

Okay, I just stumbled my way through your long-winded ramblings which at their final crescendo peaked into a flailing display of troubling numbers whose origins, and purpose, are dubious at best. My guess is that you just started pulling numbers out of your ass.

There are three different types of flagella, by the way. So if the flagella was designed, WHY ARE THEY ALL DIFFERENT? Is there more than one designer, now? You desparetly need to research exaptation. ID is such shit.

[tubewatch59]

"There are three different types of flagella, by the way. So if the flagella was designed, WHY ARE THEY ALL DIFFERENT?"

Why is there a Straight6, and V6 engines? I don't see the problem there. Variety.

Exaptation needs justification. The examples are claims, stories and homology. Exaptation seems to be the way to keep believing 'evolutiondidit' when you have run out of plausible ideas.

[massspectrician]

Aargh, what does this have to do with ANYTHING?!

[massspectrician]

'Evolution can't get you there.' Fail. You are long-winded as all hell but your conclusion don't follow from any of your premeses and furthermore are complete disjuncts of temporal logic. You are working backwards from conclusion to premise. This is NOT how to solve a problem.

[massspectrician]

'evolution is degenerative' ... fail. Total fail.

[tubewatch59]

'evolution is degenerative'

Sure is. Mutations often break things. It may enhance survival because you get a temporary benefit in a niche, typically along with the diablement of other features as a result. 1 step forward, 6 steps back.

[massspectrician]

Again with evolution dumping gene duplicates? Aargh.

[tubewatch59]

It's not absurd in extremely simple I.C. machines, because even though there cannot be a gradual pathway of intermediates preserving and improving on the core function, the possibility still exists that brute force mutation will turn up something useful. But with machines like we have in the cell the notion is really pushing the idea way beyond any repectability. Thta's why I say it's absurd and worthy of a joke. The numbers show it's not possible in any reasonable time. That shows design.

[massspectrician]

What is absurd is that you are implying that you have a grasp on the probability of such systems coming into existence, please elaborate on this (show your math). Your position involves a supernatural interloper harry pottering these systems into existence 'de novo' and ignoring the protein homologies that exist in the less-interdependent protein complexes. I see no implication of supernatural design -- I see naturalistic evolution.

[tubewatch59]

I don't have a good grasp. I can see that there are many many more ways for a system to not work than ways in which it can. Once you get to something like a flagellum the possibility of error in specifying it and assembling it are far greater than the very few ways that it could function. Remember that as an I.C. machine you cannot get there gradually. As Miller said you get there by the emergence of new functions. Big I.C. systems are too interdependant and sophisticated for that to work.

[tubewatch59]

And it's not as if natural selection is trying to get a flagellum and failing and repeating and fine tuning. No. If you accept it, then it's a different system altogether that then someghow by chance forms another different system of some kind again (that works) which then forms another system (that works) until you chance upon the end result. The finely balanced and precise I.C. machine. It just doesn't make sense. However I can see the reverse easily. Evolution disabling such machines.

[massspectrician]

Your error here is that you say the system develops 'by chance'. Natural selection isn't a random process and mutation alone is not the only evolutionary force driving development of complex machinery. Studies conducted on knock-outs which disable complex protein cascades and complexes really add to the robustness of gradual development of these systems. You just ignore this research, too, since it doesn't fit in with your preconceived notion of intelligent design.

[tubewatch59]

Cascades can be redundant. So they don't apply as they fall into the category of systems that can evolve. There are many such systems. I can't deny evolution. It is amazing what mutation and selection can come up with. But it's fundamentally a very limited process. Evolution is NOT smarter than you are. It is so dumb it tries what you wouldn't wate your time on and sometimes through btute force will find unusual solutions. But they are comparatively simple ones. That's what it can do.

[massspectrician]

Yes, but when it hits a high note, it runs with it to no end. That is one reason why it is not random, per se. I think two good examples demonstrating how evolution causes extremely rapid changes once a really kick-ass thing for survival comes in are the rapid proliferations of invertebrate shells (and other hard parts) and jaws of gnathosomes (ordovician/devonian fish).

'Cascades can be redundant ... systems that can evolve':

All systems can evolve and be redundant.

[massspectrician]

'Big I.C. systems are too interdependant and sophisticated for that to work'

Do you have an example? I think that every protein complex I've every seen sequenced and subsequently discussed in the academic arena addresses the individual component functions to dispel this kind of garbage before it is toted by the pseudo-scientific intelligent design crowd.

[massspectrician]

You just lack the scientific discipline to see how it works. You would rather rely chiefly on an imagined set of events that are completely and utterly untestable. The fact that you completely avoid your null hypothesis shows how poor your contrived notion of science is.

[tubewatch59]

Null hypothesis: I had to look that up!

That would be (correct me if I'm wrong) from the ID perspective: The observation that such machines can evolve. Or more realistically, observations that would tend to indicate that what is observed to have evolved over a realistically observable time frame, could reasonably be extrapolated to end up with functional structures such as the more complicated biochemical machines (like the flagellum, cilium, many of the others).

[massspectrician]

No.

Hypothesis: 'Biological system is designed by a supernatural interloper.'

Null hypothesis: 'System has naturalistic origins.'

We don't need to invoke evolution for your null hypothesis. Now in order to establish our hypothesis as potentially true, we have to show our null hypothesis is false. In this instance, since you can not discount that it is POSSIBLE that a system has natural origins then your hypothesis is not true. You MUST falsify, through empiricism, the null hypothesis. You can't.

[tubewatch59]

Honestly? For example:

Hypothesis: A suspect was videotaped commiting a murder. DNA at the scene matched the suspect. The suspect owed the victim money. The suspect had made threats against the victim.

Null hypothesis: The suspect is innocent. DNA matching was due to sampling from the suspect, and planting it at the scene. The videotape was an impersonation. The threats were in jest. The suspect had every intention of paying the money back. The real murderer was someone else.

[tubewatch59]

Admittedly, it's possible that this null hypothesis might actually be true. OJ. Simpson might truly be innocent as well as legally. However we do not have to disprove the null hypothesis here to entertain the notion that the suspect might in fact be guilty.

You're saying that unless we can rule out ABSOLUTELY the innocence of the suspect, we 'cannot even consider' the idea that the suspect might actually be guilty. There would always be some story that 'might' be true thwarting a conviction.

[tubewatch59]

The point is, under this criteria, no one could go to prison unless they volunteered. And then they'd likely get off because they would be declared insane. (What sane person would confess and go to prison?) If you remove probabilities from consideration, then any scenario can be brought up to explain the data. It's untestable, and isn't really science.

ID limits itself to analysing the structure of a natural system. It applies the design inference based on KNOWN naturalistic mechanisms.

[tubewatch59]

It isn't unfair because even though the designer is likewise UNKNOWN, the properties of the natural system being analysed are known and can be tested against KNOWN naturalistic mechanisms to see if naturalism is a possible explanation of the origins of the system, or whether design (by an unspecified designer (I'll call Him God)) is implicated.

[tubewatch59]

Also, since there truly is evolution of simpler kinds of enzymes etc. It should be possible to test the design inference itself in reference to these simple evolved systems. For example: Nylonase or Beta galactadose (or whatever it is) each evolved in certain fairly short periods of time involving I think, months and decades. Certainly anti-biotic resistances evolve very rapidly. The design inference can be tested to see if it predicts a naturalistic or design origin for these examples.

[tubewatch59]

In time, the design inference coupled to greater biological knowledge will fairly accurately be able to predict the approxiamte time it would take (based on populations, mutation rates etc.) to evolve certain systems. As knowledge gets more complete, the predicted time taken to evolve systems of a given level of functional complexity will be reasonably estimated. This will be when ID can be more properly tested.

eg: An evolution time of 100000000000000000000000000000­000000 yrs, is a bit long.

[massspectrician]

I think that all observed features of life fit quite nicely into an evolutionary time scale that correlates to what we see in the fossil record. Do you know how genetically homologous you are with other things in the biosphere? You are more closely related to a tree than you might think. You are closer to a chimpanzee of the same gender, by genetic homology, than you are to a human of the opposite sex.

[massspectrician]

It is natural, anti-biotic resistances evolve through mutations in plasmids. They are observed and we have the genetics to show the exact mechanism by which these processes take place. To say it is designed, well, you are just attributing a cause to something that is observed without any evidence. You could say that god causes mutation but you lose objectivity with such a claim. We don't need god because we know what mechanisms cause mutation. So does god control the mechanisms, now? Seriously?

[massspectrician]

These tests have been applied. You should really get into the literature a bit deeper if you think that anything implicates a designer did anything. Naturalistic mechanisms can explain all of this. I fear this discussion with you is taking too much time away from me actually making videos which will present this information in a concise way that you will likely agree with.

[massspectrician]

Your comparison is a little unfair. Law and science operate under different rules. ID is a conclusion-based study. It takes from the outset that things are designed, it didn't arrive at this conclusion through empiricism. It got there from a base assertion. Empiricism will never lead one to the conclusion that a supernatural entity is responsible for any outcome. More importantly what does ID teach us? How can we use it? It doesn't seem very useful to me, as well as, regressive.

[massspectrician]

I am not discounting probabilities. Only, pointing out that you don't seem qualified to perform the rigorous statistical analysis that is required to meet the scientific standard. In fact, by your above example, your grasp of very basic scientific principles seems grossly lacking.

I do have a video 'Evolution pwns Intelligent Design' posted some time ago that makes some basic arguments against the scientific merits of ID. You might want to check it out.

[massspectrician]

The standard in law is 'beyond a reasonable doubt' not 'absolutely'. In science, the standard is 'with highest confidence', also not 'absolutely'. When I talk about 'confidence' here I am referring to strict statistical analysis of empirical data.

[massspectrician]

Testing these null hypotheses:

1. Innocence: The videotape tests the null hypothesis and falsifies it.

2. DNA: NOT THE NULL HYPOTHESIS! The real null hypothesis here is 'the DNA doesn't match'. Which is tested by sequencing.

3. Debt: NOT THE NULL HYPOTHESIS! Here it is 'victim carried no debt to the accused.'

4. Threats: NOT THE NULL HYPOTHESIS! Here it is 'the threats weren't made'.

All in all, I would say you blundered your way through this example.

[bl4ckd0g187]

favorited as well. as previously stated, I think I'll favorite all of your videos on this topic, and make a playlist, which I can direct creationists to.

[massspectrician]

I am glad that you are enjoying them. Hopefully, collectively we can kill this failed argument, at least here on youtube.

[bl4ckd0g187]

yeah, but what I've noticed is that even if you present a completely valid concept, and back it up with as much evidence as possible, quite a few of them will simply deny it. it's quite odd how the creationist's mind operates.

[massspectrician]

That lot falls into the group of lost causes. I prefer to focus on the impressionable, yet rational, group among them to whom such presentation might make a valuable and lasting positive influence.

Really what I feel is necessary is to diffuse the web of lies spun by the roving bands of miscreants managing organizations like CSE Ministries, the Discovery Institute, and Answers in Genesis.

[bl4ckd0g187]

'Really what I feel is necessary is to diffuse the web of lies spun by the roving bands of miscreants managing organizations like CSE Ministries, the Discovery Institute, and Answers in Genesis.'

-which is pretty much what I think the secular community should focus on. I don't have a problem with benign religious practices; what I dislike is malignant, counter-productive (and sometimes violent) religious movements.

[massspectrician]

I won't limit myself, however. I must admit I do like to engage in profane blasphemy from time to time, as well (my debate with God, for example). But that is just for kicks. These videos are eerily remind me of, well, my job, and thus work.

[massspectrician]

I set the series aside in a playlist on my channel.