The Comedy of Errors: A Response To "Darwin Killed God" Blog (Part 2)

TheHumanApe’s blog is hardly deserving of attention, but nevertheless the job of shredding his ridiculous literature will be done.

     He devotes a number of his blog posts to providing the evidence for evolution. For example, he quotes Jerry Coyne (author of “Why Evolution is True”) on why ERVs, embryology, et al., all demonstrate the validity of common descent. He describes how fossils and protein sequences provide confirmation of common descent. However, he makes the fatal error of equating evidence of common descent for evidence of a non-directed model of common descent. He cannot accept the prospect that evolution was guided. While I am not in anyway a theistic evolutionist, there is evidence in biology that certain parts of life were involved in a guided evolution. For example, a sequence analysis of the protein alpha-importin suggests that alpha-importin in unicellular organisms would guide the evolution of beta-canenin, and with the origin of beta-canenin, multicellular life forms would arise (see Mike Gene’s blog “The Design Matrix”). If TheHumanApe stubbornly clings to the belief that even a guided evolution is  “magic,” then I’d love to hear his response to this.

       TheHumanApe gives some treatment to chromosome 2, which he calls “undeniable evidence for evolution.” He is apparently ignorant of the possibility that Homo sapiens originally had 48 chromosomes, and then a fusion reduced that number to 46. The only thing chromosome 2 proves is that homo sapiens used to have 48 chromosomes.

He comes up with even more “undeniable evidence” for evolution – namely, the evidence from DNA sequences and molecular phylogenies. He is, of course, unaware of the fact molecular nested hierarchies can be explained by tissue constraints on protein sequences. A neutral substitution in one organism is not necessarily neutral in another, due to differences in the number of cell types. As such, the evidence from DNA sequences can hardly be considered “undeniable evidence.”

I found a particular portion of his blog amusing.

 “Of course the idiot calls evolution ‘Darwinism’…. Again Christians, please read this carefully: Biologists are called ‘biologists’. It would help if you practiced saying the word "biologists" a few dozen times so you get it right next time.”

Right. It’s always difficult to get this point across to laymen like TheHumanApe: we use the term “Darwinian” to distinguish “Darwinian” evolution from Lamarckian evolution, saltationism, orthogenesis, et al. There are Darwinian biologists, there are Lamarckian biologists, etc. Biologists use the term ‘Darwinian’ to distinguish between the different evolutionary models. Of course, laymen like TheHumanApe still can’t get that straight.

Note that nowhere, absolutely nowhere, in his blog does he provide evidence against the following statement: certain features of the biological world are more adequately explained by an intelligence. He assumes that by providing a mountain of evidence for common descent, then this must mean that the flagellar motility system was not intelligently designed. One could provide all the proof in the world that humanity descended through a Darwinian process, but this would not prove that the same is true for the flagellar motility system.

One thing he said I found to be the most entertaining:

 “I left the following comment for…an uneducated moron, a typical superstitious idiot.”

I.e., I am an uneducated moron and a typical, superstitious idiot. I find that to be, in short, hilarious.

Well, I think I’ll stop it there since I don’t want to waste anymore time on something that he won’t respond to. Cheers!

The Comedy of Errors: A Response To "Darwin Killed God" Blog (Part 1)

Last night, I took a look at the comments of my blog post “Bad Design Disproves Intelligent Design? Really?” As I was reading the comments there, the aroma of nuts wafted towards my eyes – roasted nuts. Except that this guy thinks I’m nutty.

      A quick glance at his blog shook my confidence in human sanity (warning: this guy’s blog contains dozens and dozens of expletives). Of course, it’s obvious that he lacks even the most rudimentary knowledge and training in any of the biological sciences; and, for that matter, I am finding it difficult to believe that he even understands the basic methodology of science.

   In this Monday evening blog post, I will do my best not to come down too hard on this deluded atheist. Normally I wouldn’t spend my time responding to an individual of his intellectual caliber, but for lack of something else to blog about, I will make a response to particular blog posts of this guy.

   

    The first thing we notice when we go to his blog is his statement that,

 “Evolution does not need defending because it's a basic scientific fact.”

He then proceeds to write scores upon scores of blog posts defending evolution as a scientific fact. The shear volume of his textual nonsense is a remarkable testimony to the amount of time he has on his hands – time that should perhaps be used to contribute to the advancement of science, instead of rantings and ravings that simply do nothing to add to science’s advancement. The bulk of his rhetoric consists of the argument “Darwin right. Intelligent Design magic. Christians bad. Darwin right.”

Now, before we eviscerate his blog, we will respond to the comment he left on my blog.

Let’s begin.

 “Here's a translation of your gibberish that makes it more honest:

MAGIC as a scientific proposition, holds that certain features of the biological world are more adequately explained by a MAGIC MAN rather than a mindless process.”

Firstly, intelligent design does not invoke any magic. Intelligent design is a method of design detection, similar to SETI. Does SETI invoke magic? Or let me ask him the question in terms he might find more understandable:

(1)   Does the method of detecting intelligence in SETI science invoke magic?

(2)   Does the method of detecting intelligence in ID science invoke magic?

(3)   Why or why not?

Also note that ID does not define the designer, so the phrase “magic man” is silly.

 “By the way, Why Evolution is True by Jerry Coyne talks about "bad design" that makes perfect sense if evolution is true (it's true, evolution is a basic scientific fact).”

Please explain how the imperfect design of the flagellar motility system makes the origin of the flagellum more adequately explained in the light of evolution. This should be good.

 “One more thing. Magic is NOT a scientific proposition.”

I agree. Magic is not science. Intelligent design is science.

 “Scientists don't invoke magic…”

Intelligent design does not invoke magic either.

Now, we will respond to his blog with another post.

Bad Design Disproves Intelligent Design? Really?

Supposedly, bad design is a refutation of intelligent design. How is bad design and intelligent design compatible? This is one of the most common arguments raised against intelligent design, albeit one of the more egregious ones. The argument goes like this: an intelligent designer would not have designed biological system X in this way, therefore Darwinian evolution dunnit.

I think one of the first things Darwinians need to learn when attacking intelligent design is exactly what it posits. Intelligent design, as a scientific proposition, holds that certain features of the biological world are more adequately explained by an intelligence rather than a mindless process.

     So, we hold that only certain features in biology are more adequately explained by an intelligence. This alone is sufficient to overturn this argument against intelligent design. But what about flaws in the design of systems that are purported to be intelligently designed, such as the flagellum? First off, bad design is seen in objects that humans design. A broken down, badly-running watch does not indicate that it is not intelligently designed.Maybe the designer(s) of biological system X was having a bad day, and "it" made an error in designing that biological machine.

   Now we come to the philosophical argument from bad design: namely, that bad design proves that the designer was not God. Proponents of this argument ask, "If God is perfect, then how could a perfect God made a bad design?"

I answer,

P1: God is perfect, and humans are not perfect. God is omnipotent, and you are not.

P2: An imperfect, non-omnipotent being is incapable of discerning poor designs of a perfect, omnipotent Being.

P3: Therefore, we cannot assert that the design of a perfect Being is imperfect, for we are not omnipotent. 

I am expecting a response like "that's just special pleading" or "you are using the God-works-in-mysterious-ways argument." Obviously, these responses are only appeals to emotion, as they do not attack any of the premises in the above argument.

Evolution Computer Simulation Under Fire

A new peer-reviewed paper has been published by BIO-Complexity, an intelligent design journal. Entitled A Vivisection of the ev Computer Organism: Identifying Sources of Active Information, this paper demonstrates that most of the success of the EV computer simulation in finding a target, is not due to the evolutionary algorithm, but rather "the success of ev is largely due to active information introduced by the Hamming oracle and from the perceptron structure."

And,

"It is not due to the evolutionary algorithm used to perform the search. Indeed, other algorithms are shown to mine active information more efficiently from the knowledge sources provided by ev."

So, intelligent design has not contributed anything to the biological sciences, has it? I beg to differ. Undoubtedly, this paper has contributed something to science.

If you haven't noticed, there's been a lot going around with computer simulations and evolution. Consider this computer simulation that absolutely proves the flagellum could have easily evolved - one of my personal favorites:

"Dr. Jackson Martin, Director and Professor of the Flagellum Project at the Hoboken Nature Institute, today announced completion of software that successfully demonstrates the evolution of the bacterial flagellum. Critics of evolution have claimed that the flagellum is too complex to evolve using the gradual changes required by natural selection.

'The flagellum is very complicated,' said Martin. 'Like a motor, it has a rotor, a stator, and complex control mechanisms.'

Martin and his students have demonstrated, however, that the complex flagellum can be easily created using the forces of natural selection.

'We have not only shown that the flagellum can be evolved, it’s hard not to evolve the flagellum.”

In simulation software called EvolFlag, Martin and his students carefully apply gradual modifications to an initial set of boundary conditions.

Martin’s most impressive demonstration was evolution of the bacterial flagellum from common table salt.

'Salt, of course, contains no biochemicals,' offered Martin. 'The ability to evolve a fully functional flagellum from simple table salt is a tribute to the miracle of evolution' . . ."

I'm impressed.

The Reports of My Death Have Been Greatly Exaggerated

Even though I haven't been blogging for a while, the reason is not, I repeat, is not, because I have expired. The real reason is that I've been incredibly busy with academics. But never fear! Once this week is over I plan to start blogging regularly again. I hope this relieves those of you who suspected that the Darwinians had finally caught up with me and I was merely a smoldering heap. However, I also know that many of you are not relieved, since many of you would look forward to the prospect of my expiration.

Stay tuned.

Coolish New Stuff From Biology

So this will be a really quick post, mainly for those who have a passionate interest in any of the disciplines of biology. Here I'll be reporting some new areas of research from said fields.

Firstly, we have The Chaos Theory of Evolution (credits go to my friend John who showed it to me). It's an interesting read on how adaptation really doesn't explain the whole picture of large-scale evolutionary changes.

Secondly, we have a new technique in forensic science. Namely, if we have somebody's blood say, at a crime scene, we can take the DNA from the T-lymphocytes in the blood, and by an analysis of the DNA we can determine the age of that person.

Thirdly, we have research concerning glow-in-the-dark plants. Modified genes that code for enzymes that produce light in fireflies are inserted into the genome of a plant, and the plant, in theory, will glow in the dark. This may be a good source of lighting in the future.

Well, that's all for now. Stay tuned, and for those in the U.S., I wish you a happy Thanksgiving Day. For those outside of the U.S., well that just sucks.

Nah, just kidding. I wish you all a great day.

I Get A Kick Out Of Endogenous Retroviruses

I've mentioned it before. That dreaded 29+ Evidences for Macroevolution by Dr. Douglas Theobald. I took the time to examine what has been pontificated as the "smoking-gun evidence for evolution" and the "irrefutable evidence." What many Darwinians believe is the most irrefutable argument for their views is the evidence from endogenous retrovirus insertion sites. I am petrified of this evidence. In fact, I am biting my nails. After gathering a few facts, I sent the following email to Dr. Douglas Theobald, concerning this astounding piece of evidence:

 Dear Dr. Douglas Theobald,

In your 2004 article “29+ Evidences for Macroevolution” you write (Part 4: The Molecular Sequence Evidence, Prediction 4.5: Molecular evidence - Endogenous retroviruses):

   “Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent.”

You then go on to propose how this molecular sequence evidence for universal common descent could be potentially falsified:

      “It would make no sense, macroevolutionarily, if certain other mammals (e.g. dogs, cows, platypi, etc.), had these same retrogenes in the exact same chromosomal locations. For instance, it would be incredibly unlikely for dogs to also carry the three HERV-K insertions that are unique to humans, as shown in the upper right of Figure 4.4.1, since none of the other primates have these retroviral sequences.”

       Consider this molecular sequence evidence for universal common descent falsified. Essentially, in order to falsify this evidence, we must find an outgroup species that shares with a species of a certain clade the same retrogene or retrogenes insertions, but these insertion sites are not shared by the other species of that clade. This is what it boils down to.

    Interestingly enough, Barbulescu et al. (2001) have identified “a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome.”

What we have here is an outgroup species (gorilla) that shares a retrogene insertion site with a species (chimpanzee) of a certain clade (human-chimpanzee clade), but this insertion site is not shared by the other species of that clade. This alone, by your own criteria, falsifies the retrogene evidence for universal common descent you advance in your article.

    

      Similarly, Bonner et al. (1982) report that the endogenous retrovirus colobus type C virus CPC-1 is shared by the chimpanzee and the gorilla but it is absent from the human genome.

Also note that certain classes of type C retroviruses are found in wooly monkeys and the gibbon ape, but it is not found in African great apes [Lieber et al. 1975].

     Humans and Asian apes lack PTERV1 retroviruses, but they are present in African great apes and Old World monkeys [Yohn et al. 2005].

  To quote Yohn et al. 2005:

“For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee.…If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely.”

In summary, the very criteria that you stated would falsify this evidence for universal common descent has been met, and hence this evidence is effectively falsified. I am writing you so that you might add a correction to your article and realize that this evidence has been falsified.

Respectfully,

Livingstone Morford

References:

Barbulescu M, Turner G, Su M, Kim R, Jensen-Seaman MI, Deinard AS, Kidd KK, Lenz J. A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans. Curr. Biol. 11(10):779-83 (2001).

Bonner TI, Birkenmeier EH, Gonda MA, Mark GE, Searfoss GH, et al. Molecular cloning of a family of retroviral sequences found in chimpanzee but not human DNA. J. Virol. 43: 914–924 (1982).

Lieber MM, Sherr CJ, Todaro GJ, Benveniste RE, Callahan R, et al. Isolation from the Asian mouse Mus caroli of an endogenous type C virus related to infectious primate type C viruses. Proc. Natl. Acad. Sci., 72: 2315–2319 (1975).

Yohn CT, et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol, 3:110 (2005).

There. Now I've gotten this load off my chest. That's some absolutely amazing piece of evidence.

The Tangled Web: Darwinian Evolution and Morality

Of late, my friend Chris has been blogging about the moral argument for the existence of God. Atheists typically respond to the moral argument by saying that morals evolved. While some very good refutations of that view are available, I wish to add my own comments regarding the atheist position. I'll tackle that position from the angle of genetics and not philosophy et al.

First off, is it morally acceptable for a member of the species homo sapiens to kill another homo sapiens without cause? Not at all, and most people, including atheists, will agree with me. So, here's another question: is it morally acceptable for humans to kill chimpanzees, for no reason other than, say for the chimpanzee's fur? If the answer is "no," then is it morally acceptable to kill (without cause other than profit) a gorilla? A lemur? To get to the meat of my argument, at what percent of DNA similarity to our DNA does it become morally acceptable to kill an animal for no real cause? Are we allowed to kill an animal whose DNA is say, 99.99% similar to our own DNA? Is it okay to kill an animal whose DNA is 98% similar to our own? 97%? You see, if morals evolved without any guiding intelligence, at what percentage of DNA similarity are we supposed to draw the line that separates those creatures that we may kill and those we may not kill? Something to ponder over. After all, we share 97.5% similarity to mice [Mural et al. 2002], and yet, intriguingly, tonight I am setting up some mice traps to catch those nasty pests. So, I would love to hear an atheist response to this. 

References:

R. J. Mural et al. A Comparison of Whole-Genome Shotgun-Derived Mouse. Science 296: 1661 (2002). 

Thinking About Theology

For today's article we will cover a series of questions usually posed by skeptics. I (Livingstone) will be L and my guest speaker Christopher will be C.

L: Tell me how do we know, as believers, that Christianity is true?

C: A number of philosophers have struggled with this question, such as Thomas Aquinas and John Locke to name a few. They asked "do we know Christianity is true by the arguments or by experience." Well Alvin Plantinga gave a good answer which I think is sound. He argues that belief in God is a properly basic belief. If one experiences God and his cognitive faculties are in their appropriate circumstances then one can know God exists. Plantinga extends that argument to Christianity, saying that the Holy Spirit is a cognitive faculty: when the unbeliever as well as the believer is experiencing the Holy Spirit and his cognitive faculties are in the appropriate circumstances one can know Christianity is true.

L: I hear you a mentioning cognitive faculties. What are they exactly?

C: Sorry for not making my terms clear. In a nutshell they are belief forming mechanisms.

L: So explain the argument in simpler terms in case our reader didn't understand it.

C: I would love to. When one's cognitive faculties (belief forming mechanisms) are in their appropriate circumstances one can know God exists. To give an analogy suppose I see a tree and now I believe the tree exists. I know the tree exists because my cognitive faculties were in the appropriate circumstances: namely being in front of the tree and experiencing it. Since I was in the appropriate circumstances I can know the tree exists. Now if I experience God and I am in the appropriate circumstances I can know God exists.

L: Ah I think I see now what your saying. Basically if we are in the right place in the right time and our cognitive faculties are functioning correctly we can know God exists?

C: Something like that.

L: So Chris how are we warranted in our belief?

C: Good question! Now let's go back to our analogy of the tree. Say that we go to our friend and try to convince him of the tree's existence. He then gives you very powerful arguments to convince you that the tree does not exist. Does that mean you will say well I guess I was wrong the tree doesn't exist! No! There is almost a defeater in you that no matter what you know you're right! Like a thief who says he isn't given in court powerful evidence that he is guilty does that mean he should say I am guilty?! No! So same thing with God: when we are given a argument we need not be troubled because our experience is so powerful that we know we are right.

L: So it seems to me that believers rely on experience to know God exists? But how then do we convince the unbeliever God exists?

C; Excellent question! To us believers experience is the way we know God exist namely through the inner witness of the Holy spirit. But to unbelievers arguments and evidence can show Christianity is true. So to believers we know God exists through the inner witness of the Holy Spirit but we can show Christianity is true by the arguments and evidences. And the arguments and evidences to believers strengthen our faith.

L: Okay next major question. How does God and evil exist?

C:Well there are many arguments to answer this. To name a few the free will defense, and the middle knowledge defense. But note here when the unbeliever presents this argument he is presupposing that objective evil exists. So he is affirming that there is such a thing as good and evil and right and wrong. But in order for those things to exist God must exist. We can lay this counter argument in the following way.

1. If God does not exist then objective moral values do not exist.
2. Objective moral values do exist.
3. Therefore God exists.

L: So basically even though the problem of evil seems to disprove God existence, it actually reinforces it?

C: Ironically, yes!

L: Okay move on to our next question. There seems to be a lot of misconceptions of God's nature. Would you mind clearing some up? Namely, omnipotence.

C: I would be glad to. First off, many people think that God can do anything. Well that is false there are two things God cannot do: 1. The logically impossible 2: Sin. God cannot do the logically impossible. Such as a round square or a married bachelor. So when atheist reply -- "Can God make a stone so heavy he can lift?"-- that is a meaningless question because that state of affairs is logically impossible. And the Bible teaches that God cannot lie or sin, since it is against his nature.

L: So can you give us a definition of omnipotence?

C: I would be happy too. Omnipotence is God being able to do anything that is logically possible and doesn't contradict his nature.


L: Thank you Chris for being on my blog  today and if you want to check out Chris's blog you can go to here or you can visit his Youtube page.

My Response To Dryden et al.

The science journals appear to have come up with a clever strategy to keep papers critical of Darwinian evolution out of the peer-reviewed literature: simply reject the papers or letters to the editor on the grounds that "your response would not be of interest to our readers.” This is evidenced by the refusal to publish Michael Behe's responses to various papers. In short: if you're critical of a paper that attempts to explain a problem for Darwinian evolution, then your paper is not interesting, and hence it won't be published. It's a neat trick, and one that I suspect I fell for.

         First off, I submitted a manuscript to the Journal of the Royal Society Interface. My paper was a critique of a paper by Dryden et al. 2008, "How much of protein sequence space has been explored by life on Earth?" In this paper, Dryden et al. argue that by reducing the functional amino acid repertoire, to, among others, a binary amino acid alphabet consisting of hydrophobic and hydrophilic amino acids, then evolutionary processes can easily navigate the whole of functional protein sequence space. Consider that for a protein only 100 amino acids in length, there are 20^100 potential amino acid combinations. By reducing the functional amino acid alphabet to one consisting of only hydrophobic and hydrophilic amino acids, then protein sequence space has a potential of only 2^100 functional sequences. Essentially, they argue that the only thing that matters for a protein to function is that the protein has the right sequence arrangement of hydrophobic and hydrophilic residues. They try to reduce the amino acid repertoire through other means, but the point is this: the paper is nonsense. There are many glaring errors in that paper, some of which I point out in the response I submitted to the Journal of the Royal Society Interface (I submitted the manuscript on August 28, 2010).

Well, gee, but ten days later I received the journal's decision regarding my paper. It shouldn't be hard to guess why they rejected my paper.

Here's a hint: it's not because the reviewers sent a rebuttal to my paper, and it's not because my paper made some error in biology.

So, anyway, here's why they rejected my paper:

"Thank you for submitting your manuscript entitled "On the Reduction of the Amino Acid Repertoire in Functional Protein Structures" to J. R. Soc. Interface.

...Many more good manuscripts are submitted to us than we have space to publish, and we give preference to those that present significant advances of broad interest. Unfortunately, your manuscript has been rejected at this stage, as it was not considered to have sufficient appeal for the general readership of J. R. Soc. Interface."  [emphasis added]

Okay, I'll admit that my paper did not represent any real experimental research. But interestingly enough, Dryden et al.'s paper wasn't an experimental paper either, but purely theoretical. However, since I guess it had sufficient appeal for the general readership of the journal, it got published. No problem.

Oh, and I forgot to include this last line the journal sent me:

"Thank you for your paper and I hope that it will be published elsewhere." That makes me feel better.

   Now for those of you interested in my critique of Dryden et al.'s paper, I will link to my response at the end of this post (too bad, but my paper didn't refer to some fairly recent work that further supports my paper).

Here's the abstract:

Abstract

It has been postulated by Dryden et al. [Dryden David T.F, Thomson Andrew R, White John H. How much of protein sequence space has been explored by life on Earth? J. R. Soc. Interface, 5,25:953-956 (2008)] that the amino acid repertoire of functional protein structures may be reduced to a binary one consisting of hydrophobic and hydrophilic residues without affecting protein function. Moreover, they point to proteins with a low degree of functional complexity and posit that such structures demonstrate that the actual identity of most of the amino acids in a protein is irrelevant. They conclude that, as a result of such reduction there is no role for molecular contingency, and furthermore that potential functional protein sequence space is completely explorable.

        Here, based on presented data and through a protein sequence alignment, it is shown that the stated postulate does not hold. For this reason, I conclude that there is a role for molecular contingency and not all of functional protein sequence space has been explored by life on earth.

Here's the full paper:

On The Reduction of The Amino Acid Repertoire In Functional Protein Structures.

And finally, here are all the beta-tubulin sequences I aligned from 30 different organisms (that took quite a toll on my hands):

Beta-tubulin sequences.

Now I have to go and revise a paper that I'm having a little better luck with. And I have to go eat a sandwich because I actually am not a robot behind a computer screen, contrary to popular opinion.

The finishing touch to this will be two quotes from two different Darwinians:

"...at the molecular level, there is no role for contingency."
-Dryden et al. 2008, "How much of protein sequence space has been explored by life on Earth?"

"... historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection."

-Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A 105(23):7899-7906.


Addendum:

In my paper, one of the conserved residues in beta-tubulin is cys-12. Since this residue is conserved in all thirty organisms, one would predict that this residue is critical to beta-tubulin function. This prediction is confirmed by site-directed mutagenesis of this residue by Gupta et al. 2001:
"The results suggest that the C12 and C354 residues play important roles in the structure and function of tubulin."

Gupta ML, et al. Mutagenesis of beta-tubulin cysteine residues in Saccharomyces cerevisiae: mutation of cysteine 354 results in cold-stable microtubules. Cell Motil. Cytoskeleton, 49(2):67-77 (2001).

Giving Both Barrels: A Two-Part Response To Professor Larry Moran, Part 2

        Unfortunately, Professor Larry Moran has been caught quote-mining in his blog post God Plays Bridge. And he doesn’t save the best for last: he quotes-mine right at the start. In case he accuses me of quote-mining, I will quote the Prof’s quote-mine (this blog post is not intended to be a tongue-twister regardless of what you might suspect):

“The creationists tell us that anything in biology with a probability of 10^39 or less is impossible.”

I searched and searched the web and didn’t find any sites saying that a biochemical system with a probability of origin less than 10^39 is more adequately explained by an intelligence, so I can confidently conclude that Prof. Moran is referring to what I said, and only to what I said (I suspect that in lieu of being caught quote-mining Prof. Moran will attempt to claim that he wasn’t referring to what I said per se’; we shall await further developments). So, where does he quote-mine me?

For starters, Prof. Moran confuses “impossible” with “intelligent design is a more adequate explanation.” What I said precisely was this,

“intelligent design proponents need only demonstrate that the odds of a particular biochemical system evolving are 10^-40 or less in order for intelligent design to be a more adequate explanation for the origin of such a biochemical system.”

Where did I say that if the odds of a particular biochemical system evolving is 10^-39 (or for that matter 10^-40) then it is impossible (to evolve I suppose is what Prof. Moran meant)? I did not say such a thing; I only said that in such a scenario intelligent design is a more adequate explanation for the origin of that system.  Either I’m aging far sooner than I expected and Prof. Moran is seeing something I said that I can’t see or Prof. Moran is quote-mining. Take your pick.

This quote-mining business gets even more interesting when we see that Prof. Moran himself condemns quote-mining and has a lot to say about this dirty business (here, here, here, and here). Talk about double standards.

Anyway, Prof. Moran tries yet again to refute my argument regarding the probability of a Darwinian origin of biochemical systems, this time using a bridge game as an analogy (incidentally, I don’t play bridge). I believe I sufficiently responded to his analogies with a reference to a peer-reviewed paper, and once again I will remind our dear professor that his arguments contradict the very arguments advanced for common descent; namely, the argument from ERV insertion sites.

I wonder if Prof. Moran plays bridge? If he does, I wonder if that was when he thought up that lovely quote-mine?

Giving Both Barrels: A Two-Part Response To Professor Larry Moran, Part 1

    I had the guts to make several comments on Professor Larry Moran’s blog, Sandwalk; he has responded to one of these comments with two blog posts (here and here). And now, I have the chutzpah to respond to Professor Larry Moran (to get the gist of what’s going on see my comments on Sandwalk) on BioTalk.

The comment to which Prof. Moran responded to was pretty straightforward. Namely, I argued that “intelligent design proponents need only demonstrate that the odds of a particular biochemical system evolving are 10^-40 or less in order for intelligent design to be a more adequate explanation for the origin of such a biochemical system. This is because there have been no more than 10^39 bacterial cells in the history of life on earth.”

       

    Prof. Moran contends that the above argument cannot possibly hold much water, and he attempts to substantiate that assertion by bringing up the following argument:

That the odds of a specified sperm uniting with an egg is deplorably low, and as a result, through various calculations he does, he concludes that the probability of his four great-grandparents being born is lower than 10^-64 – a probability significantly lower than my stated 10^-40.

     

        Unfortunately by arguing thusly our dear professor is opening a can of worms for the entire common descent framework in that he is tacitly “refuting” the evidence for common descent. One of the oft-cited evidences for common descent are the shared insertion sites of endogenous retroviruses between humans and chimpanzees. However, if we are to accept Prof. Moran’s dictum that something having a probability of occurring of 10^-64 is in fact perfectly plausible, then we must accept that it is perfectly plausible that the shared ERV insertion sites between humans and chimpanzees may be the result of mere coincidence. Prof. Moran is trying to have it both ways but that is a of course a  blatant contradiction.

       

   Moreover, I would like to ask Prof. Moran to please explain to me in terms of probability, why precisely polyvalent antimalarial treatments are more effective than standard treatments? It seems as if Prof. Moran is wishing to go against the peer-reviewed literature, where we see that White (2004) says,

"If two drugs are used with different modes of action, and therefore different resistance mechanisms, then the per-parasite probability of developing resistance to both drugs is the product of their individual per-parasite probabilities. This is particularly powerful in malaria, because there are only about 10¹⁷ malaria parasites in the entire world. For example, if the per-parasite probabilities of developing resistance to drug A and drug B are both 1 in 10¹², then a simultaneously resistant mutant will arise spontaneously every 1 in 10²⁴ parasites. As there is a cumulative total of less than 10²⁰ malaria parasites in existence in one year, such a simultaneously resistant parasite would arise spontaneously roughly once every 10,000 years — provided the drugs always confronted the parasites in combination. Thus the lower the de novo per-parasite probability of developing resistance, the greater the delay in the emergence of resistance.”

Now, to support my assertion that it is implausible to expect Darwinian processes to produce a biochemical system having a probability of origin less than 10^40, we must merely use a little logic.

If the per-E.coli probability of evolving biochemical system A is 10^40, then a mutant E. coli with this biochemical system will arise every 1 in 10^40 cells. As there is a cumulative total of about 10^30 bacterial cells in existence in one year [Whitman et al. 1998], such a mutant E. coli would arise roughly once every 3.55 billion years.

      Sound familiar? I’m using the exact same math that White 2004 is using, yet amusingly I don’t see Prof. Moran talking about how the referee(s) of White’s paper messed up in their review of his paper; nor for that matter do I see him criticizing N.J. White’s work; nor for that matter have I seen a letter from Prof. Moran to the Journal of Clinical Investigation correcting White’s work. I wonder why that could be? Oh right, I forgot, I’m advocating intelligent design so only I can be wrong when I use the same reasoning a peer-reviewed paper uses. Neat, isn’t it?

References:

1. White, Nicholas J. Antimalarial drug resistance. J. Clin. Invest, 113(8):1084–1092 (2004). 

2. Whitman W.B, Coleman D.C, Wiebe W.J. Prokaryotes: the unseen majority Proc. Natl Acad. Sci. 95(12): 6578-6583 (1998). 


Addendum: I said that,
"If the per-E.coli probability of evolving biochemical system A is 10^40, then a mutant E. coli with this biochemical system will arise every 1 in 10^40 cells. As there is a cumulative total of about 10^30 bacterial cells in existence in one year [Whitman et al. 1998], such a mutant E. coli would arise roughly once every 3.55 billion years." 

I might add that " thus the lower the  per-E.coli probability of developing biochemical system A the greater the delay in the emergence of biochemical system A", a statement consistent with White's paper.

When A Neutral Mutation Isn't

It has long been assumed in Darwinian circles that a neutral substitution in a protein is neutral in any given organism. In other words, a neutral substitution in a protein will be neutral in the human variant of that protein as well as the yeast variant of that protein, and in the amoeba variant of that protein, etc. So how did I found out that there is this assumption in Darwinian thinking? I peeked. Actually, I peeked a long time ago at Dr. Douglas Theobald's "29+ Evidences For Macroevolution (please do not ask me where he came up with the fascination with the number '29')." One of the things he said is telling of the assumption I described above. And this assumption is echoed by none other than Mr. Randy Crum! Since Mr. Crum actually describes it in more audience-friendly prose, I will quote Carumbas Blog yet again (click here to see Dr. Theobald's own words).

Thus sayeth Mr. Randy Crum (I will try to make this the last blog post where Mr. Crum takes flack, in case any of you are feeling sorry for him):

"In the last few decades, scientists have been able to sequence DNA and determine the specific amino acid sequences that make up proteins. Some of these proteins are very important and are present in all living things. But in many cases not every amino acid is necessary. Evolution predicts that differences will be explicable through evolutionary history.

The best way to explain this is through an example. The prototypical example is cytochrome-c.

Cytochrome c is an absolutely essential protein found in all organisms, including eukaryotes (organisms with cells that have a nucleus) and bacteria. It is necessary for life in all organisms because it allows mitochondria - the energy fuel of cells - to function.

Much of the cytochrome c protein is not needed (it is “functionally silent”). That part varies from organism to organism. Human cytochrome c has been confirmed to work in yeast - a single-celled organism - despite the fact that the naturally occurring cytochrome c found in yeast is very different from that found in humans (sharing only 38 amino acids)."

Okay I'll have to digress for a bit here. Mitochondria actually isn't the "energy fuel of cells" as Mr. Crum claims, but rather the ATP molecules are. 

Anyway this assumption I spoke of earlier is very prevalent in Darwinian circles. And what's wrong with this assumption? Well, to put it in terms that you would all understand, this assumption is simply wrong. 

The evidence from protein sequences convinces me of this. The error in this assumption is that it does not take into account organismal complexity, i.e. the number of different cell types in an organism. A yeast cell for example has only one type of cell, but the human organism has many different types of cells, from neurons to fat cells to erythrocytes. And this has rather profound implications. A neutral mutation in a yeast protein may not be neutral in humans. Here's why:

An ontogenic amino acid substitution in a human protein must be compatible with every one of the different cells found in the human organism (every cell, that is, that contains the protein; actin is prevalent in most human tissues, to name one example, while hemoglobin is found only in erythrocytes), while an amino acid substitution in a yeast protein must be compatible with only one cell type. 

An analogy may (in a theoretical sense) be useful here. Say you have protein A. And you have cell type X, Y, and Z. Any substitution mutation in protein A must be compatible with all three cell types. Meanwhile, if you only have cell type X, then protein A needs only to compatible with X (analogy a la Dr. Shi Huang). 

Now, the idea that a neutral mutation in yeast is not necessarily neutral in say, humans, is consistent with observations from cytochrome c sequences.

I compared the cytochrome c sequence of two unicellular organisms: Naegleria gruberi and Dictyostelium discoideum. To guard against any deletions, insertions, and what-not that might influence my sequence alignment I used the dot-matrix approach (Figure 1) as well as using ClustalX for the alignment.

The dot-matrix method found nothing that would significantly influence the alignment, although after correcting for gaps I achieved what I believe is the best alignment of the cytochrome c sequence of the two unicellular organisms (Figure 2).

Next, I aligned the cytochrome c sequence of two organisms as distant as the tuna and humans. The dot-matrix approach revealed a deletion as well as a higher degree of sequence similarity (Figure 3) than that between the two unicellular organisms. For a more quantifiable degree of sequence similarity between tuna and human cytochrome c, see Figure 4.

From the dot-matrix alignment and the ClustalX alignment one can see that there is obviously more sequence conservation in human and tuna cytochrome c than in the cytochrome c of the two unicellular organisms. This is what would be expected if a substitution in a unicellular organism was not necessarily neutral for a multicellular organism. I will add here that while human cytochrome c functions perfectly fine in yeast, no experiments have proven the reverse: I highly doubt that yeast cytochrome c would function in humans. I would predict that any protein from a multicellular organism would also function in a unicellular organism, but not vice versa.

Indeed, throughout the biological world we see conservation of protein sequences in multicellular organisms while there might often be a lack of conservation in unicellular organisms. Also, if one found a protein sequence that was conserved in unicellular organisms but not conserved in multicellular organisms then the entire idea I am proposing here would be proven utterly wrong. But there's not a single example of that, which would seem to validate this idea (an idea first proposed by Dr. Shi Huang I believe).

I suspect the Darwinians would respond with something like this: unicellular organisms reproduce faster than humans and tuna so they have had more time to accumulate neutral mutations. This however contradicts the notion of a constant clock, opening a can of worms for the Darwinian hypothesis.

So what are the implications of this? Namely, that one cannot really arbitrarily argue for a Darwinian origin of life forms on the basis of functional redundancy in proteins, since what is functionally redundant in one organism may not be in another.

I guess I'd better sit down and start working on a technical paper along these lines. And try not to feel sorry for you-know-who.

How To Build A Strawman And Knock It Down

This morning I got up and turned my computer on. I began randomly browsing the web, glass of water in hand. I almost choked to death. Carumbas Blog got my attention. According to that blog, intelligent design can never be science because intelligent design isn't falsifiable.

To quote the author of the blog:

"ID cannot be science because it can never be falsified – a requirement of a scientific hypothesis. ID never can be falsified – and therefore cannot be science - as long as one possibility for the designer is an omnipotent and omniscient God. Such a God, by definition, can do anything and do so for reasons that we mere humans might not be able to understand. As long as such a God is a possible designer – even if not the only possibility – any natural phenomenon is possible. Because of that, until the possibility of an omnipotent and omniscient God is specifically excluded as a possible designer, ID cannot possibly be science."

Right off the bat Randy Crum (the author of the blog) gets it wrong. What we essentially have here is Mr. Crum constructing a man made out of straw and then proceeding to destroy it. Let's deconstruct his straw-man.

   To do this, we need to define intelligent design. In a word, intelligent design holds that certain features of the biological world are more adequately explained by an intelligence rather than a mindless process like Darwinian evolution.

 So can intelligent design be falsified? You bet. If for example one observed the evolution of a biochemical system that required several dozen specifically arranged amino acid residues, then intelligent design proponents would stay up till 4 o'clock in the morning pondering over how they could have messed up so badly. Mr. Crum of course, by his argument, would argue that this wouldn't really falsify intelligent design because if an omnipotent God was the designer, then the designer could "do anything and do so for reasons that we mere humans might not be able to understand." However this is fallacious because it is irrelevant whether or not the designer did things we could understand; what is the real issue here is whether intelligent design is a more adequate explanation for something in the biological world than a mindless process. Even if God decided to allow such a described biochemical system to evolve in real-time, intelligent design would still have been falsified because to us humans intelligent design would cease to be a more adequate explanation for the origin of said biochemical system. 

And I thought Darwinians didn't use straw-men arguments. 

Getting The Feel of It: Introducing BioTalk

So folks this is in fact my blog. My name is Livingstone (don't ask me why). What's this blog all about? Well, first of all it's biological ramblings that will cover all aspects of biology from evolution and intelligent design to my thoughts on bioethics and the latest news in biology et al. You get the idea. This blog will also every now and then delve into what's going on in my own life and stuff like that.

   As this will be a blog primarily focusing on topics in the biological disciplines (most often biochemistry, of course) I will do my best to make the reading experience as painless as possible. Technical terminology will frequently be used and those without a technical background will probably be oblivious to what I am trying to say.

Thus, I am outlining the following, step-by-step guide of what to do in case you are completely and totally lost in the dense undergrowth of the technical world:

1. Relax. Take a deep breath.

2. Immediately after stumbling through one of my posts, get up and stare out the window, watching the cars and people go by, until the fogginess in your head clears.

3. Sit down and go to the comments section on this blog. Type out any questions you have regarding a post I have made.

4. I will respond to your inquiries and attempt to clear some of the haziness. Your inquiries are encouraged, and if I post an extremely technical piece of literature, and there is an absence of questions, I will be confident that no one is reading my blog anymore.

5. If all else fails, relax.

The comments section are there for the purpose of being used, so feel free to type out a 1000 word response to my post. Debate and civil discourse is encouraged, but keep it civil. Moreover, I have no sympathy for trolls and they will be dealt with appropriately.

So there you have it folks!

Introducing BioTalk! Ta-da!