Friday, October 29, 2010

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?

Thursday, October 28, 2010

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?


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.

Tuesday, October 19, 2010

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.

Sunday, October 17, 2010

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. 

Saturday, October 16, 2010

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!