CharonY

Well, I do not think that there is anything hindering progress except the complexity of the system itself. However, funds are limited. In many cases the functions can only be studied in detailed in animal models, with all its ethical and financial implications, for instance. Knowing that an area is active/silenced for instance tells you nil about the function of it. Just to make my point clear, the genome of E. coli has been sequenced years ago, every single (non-essential) gene has been knocked out in a mutant library or another. It is arguably the most genetically accessible organism we have. Yet roughly 25% of its genome has an unknown function. The reason is essentially very simple. To date the way to infer function is to knock the gene out see phenotype changes and ideally also associate it with activity changes. So you knock out a gene, the strain becomes heat sensitive and in other experiments you see that the gene gets induced under heat stress. Ergo: the gene is involved in heat stress response. However, as you can easily imagine there are virtually unlimited stimuli around that you could test. Worse even cells have the habit to compensate for mutations that you introduce so that most experiments are not clear-cut that way. Cells have to respond to any number of internal, as well as external changes. The big hope of the postgenome era was that highthroughput data would eventually give a complete view of what is happening in a cell. To date it isn't. You can see what is happening (within the technical restrictions) but the story they tell is sometimes almost as complex as the cell itself.

Sure, though an additional point would be that gene loss and gain events are not really good as distance markers. One of them is simply the identifying those events, another is that the rate of the turnover can be very hard to estimate (the actual point of the paper). Another, possibly more important point might be that it is a complete waste of time. Traditionally ID/creationism proponents rarely do respond to corrections or any arguments. This is sadly also true to some extent to those who actually "believe" in evolution, without actually a deeper knowledge in that matter. And mind you, evolution is a bloody complicated matter since it has departed from the more intuitive Darwinian basics (I am a biologist involved in genomics, though I lack the knowledge of a true evolutionary biologist in that matter). Imagine, for instance, the integration of a virus into the genome. Let us assume furthermore that around 1kb of the virus remains stably in the genome of a population. Now comparing those with and without the virus would yield 1000 additional bases. This is simply not comparable to 1000 individual point mutations. Again the paper's work was not to estimate distances per se, but its point was that in humans they claim to have found an accelerated gene turnover (that is, duplication events and gene losses).

Well and technically one of them is a triglyceride.

In the Y chromosome a lot of genes are effectively silenced. As such a YY karyotype is probably not viable. XYY occurs, though.

No, the article only claims that there are an estimated 1418 genes (mind you, it is just an estimation!) of 1418 genes that are not 1-1 orthologous to each other. Does it mean that there are 6% genome difference? Hell no. Let us do some very basic calculations. The average gene size is roughly 3kb. If we assume (as we do not really know yet!) that there are 22k genes in the human genome, we come to a total sequence size of around 22k x 3kb = 66MB The human genome is roughly 3000 MB, so the gene content only account for roughly 22 % of the whole genome. Moving on. 1418 gene difference (~ 4MB) would therefore to account for 0.1% sequence diversity. Quite a difference, right? Also he apparently did not quite get the gist of the publication. Or at least chose to misinterpret it. Mind you to calculate whole genome distances is quite complicated. What the paper did, however is to investigate gene loss/gain events, or rather the rates rather than the absolute distance. I just took a look whether this Peter Borger guy is real. Unfortunately he is, though I do hope that he did not really make his PhD in biology (biochemistry would be alright, though). He apparently is affiliated with the ISCID, a group involved in promoting ID (Behe is in the editorial board, btw). Dear me.

Well, yeah. IIRC they reported an enhanced growth of Cryptococcus species. Though the reason for it is still unclear.

Nope, the transfers occur because the phages do not always package in the right DNA. As such you cannot easily control whether the bacteria you are targeting might not get something that makes them more virulent. Also, viruses can mutate very easily. Regardless, as they replicate you cannot control the dosage, regardless with which specificity. Phage production is also pretty tricky, make no mistake.

I am too lazy to type something up on my own, especially as Sisyphus has already answered so well. There are even some alleles that are associated with homosexuality, but they do not determine it completely. I do not recall the details but in at least on study the same allele was associated with higher fecundity, offering an explanation why this allele might persist even if it should promote homosexuality. In any case, I am an anonymous internet-poster and I endorse Sisyphus' message.

Well bacterial fuel cells have been around for some while. Essentially they couple oxidation processes by transfers of electrons to electrodes. In other words, they use electrodes instead of standard electron acceptors. However they generally only work with anaerobic bacteria, as aerobes use oxygen instead (and generally won't grow on electrodes). Cyanobacteria do not grow on electrodes though, therefore this kind of fuel cells do not produce electricity, but they are used to produce lipids as a basic for biofuels. Same words but different meanings. That approach (as well as biogas) is actually rather promising, it is in essence an upscaled fermenter. Fuel cells for direct generation of electricity are still far too inefficient and costly (as you have to put in electron donors in the first place), to be practically usable.

Without getting into details, I am not sure what kind of phd he holds but this is rather ridiculous. First we do not know the genes in the human genome yet. The 25k or so are just estimates. Identifying genes in a genome is a daunting task and neither in human or chimpanzee it is near completion (if it can be completed at all). A number of 1400 different genes can only be an estimate of an estimate. Even worse, what qualifies as a different gene? For relation purposes the only relevant value is the amount of sequence differences (including indels). Summarizing, distance can only be estimated by sequence differences, counting genes is ridiculous and apparently there are cheap phds out there. good night.

Unless you learn to compartmentalize it might be slightly tricky if you are a biologist and follow a religion that involves creation of life. I assume that most physicists or chemist would not have any problems, though.

Actually almost all bacteria (or cells in general) have a certain amount of UV resistance, otherwise they would not be able to withstand sun radiation. The degree varies extremely between species though. One of the most radiation resistant ones (to my knowledge) is Deinococcus radiodurans. However, all resistances are dosage dependent.

What precisely do you need help with? What is it that you understand/do not understand?

Yupp. It is a misconception that all organisms require oxygen. The first ones did not and in fact the occurence of oxygen (due to photosynthetic bacteria) led to one (if not the) largest extinction of (bacterial) species in the early history of earth. Oxygen is but only one of many terminal electron acceptors.

Precisely. A water molecule (H2O) has different properties than oxygen (O2), regardless of their respecitive state (be it solid, liquid or gaseous). Oxygen was introduced much later due to biological activity into the atmosphere.

Hmm: Obama 86% McKinney 78% McCain 75%

Without further analytical tests you wouldn't know what kind of bacteria you got (pathogenic or no). At least not until it is too late . Do you mean incubating your plates in the basement? It depends on the bacteria. There are of course a number (actually most) that would grow below body temperature, but they grow slower. Your plates might dry out during that time. Also contamination would be a problem.

First of all blood agar is a form of nutrient agar. However, every nutrient agar, be it complex ones like LB, BHIS, BAP, chocolate, etc. or minimal media will only allow a certain range of bacteria to grow on it. The complex media obviously tend to have a broader range, though. In any case, bacteria growing on or in hosts are often cultivated with nutrients that the host have to offer, hence often blood agar or BHIS is used. Howeever for oral bacteria one could also use THB, MM10SB, to name a few.

Dito. Incidentally I found an article referirng to that incident: http://www.cnn.com/2008/POLITICS/10/13/campbell.brown.obama/index.html Boy, I browse so much, I must be writing a paper

If you are interested in the marginal tax rate (just to stress it, it is the marginal tax rate) below 25,000 here is another calculations, which also takes in McCain's proposal: http://taxprof.typepad.com/taxprof_blog/2008/10/marginal-tax-ra.html Is it just a coincidence that the sharpest drops in marginal tax rate in Obama's plan are not included in the above posted chart?

True that. The exchange went something like. "He is an Arab" "No Ma'am he is a decent person". It probably wasn't meant that way, but it is pretty insulting anyway.

I used my tablet. But I found out that I wrote too fast as compared to using the blackboard (non-digita that is...).

Actually there are very good textbooks that explain the basics of statistics (e.g. kinds of distributions etc.). I cannot name one out of my memory, but they often have titles like "statistical methods for medical research", "statistics for life sciences" or suchalike. I would not be surprised to find a "biostastics for dummies" either. Quite often they are a bit better than websites as they tend to be more coherent and ground up.

Actually there are quite a number of disadvantages: 1) specificity. Phages often have a very narrow host range, so one hast to be very sure which bacteria are to be targeted. Even so there is some chance that the specific strain might be resistant. 2) it is not always easy to maintain the phages in a lytic cycle. 3) as already mentioned, the risk of phage induced horizontal gene transfer. With some bad luck you may transfer pathogenicity genese to otherwise harmless bacteria, thus worsen your condition 4) getting purified phage preparations that are free from bacteria is not that trivial or cheap 5) dosages are hard to maintain due to the replicative nature of the virus That are just a few that I can think of right now. I am sure there is more.

Ouch, that is what happened on my first lecture here (also using blackboard). Also I learned that if you upload the lecture as pdf, convert it into the oldest formate you can find. Quite a number are not able to update the reader to the current version. Or the version from last year.