Thursday, November 25, 2010

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.

Tuesday, November 16, 2010

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.

Livingstone Morford


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.

Thursday, November 11, 2010

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. 


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

Friday, November 5, 2010

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.

Thursday, November 4, 2010

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:


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:

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

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:

" 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.


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).