CharonY

Let us go back to this claim Note that at this point we are talking about information content of search algorithms. Not about information per se. That being said it is true that averaged over all possible landscape no algorithm outperforms a random walk. A rather obvious observation. Algorithm only performs well in specific search spaces- no surprise there. Averaging over all search spaces results in identical outcomes to each node and thus each choice would lead to the same result. So what it basically boils down to is that certain search algorithm perform better in specific search spaces and not at all in others. Surprise! It has been postulated much earlier that search algorithms do not generate information but merely transform it. This does not really provides deep insights, the only interesting bits were the attempts to quantify the content, in which a rather abysmal job was done. There must be a place for dull papers, too, I guess. Now what he tries to do (not in peer-reviewed publications from what I can see) is to apply this to evolution and here is where he fails. Even disregarding the problems of trying to model evolution as a search, Dembski overlooks some very basic facts. The single most important element is that evolution does not work on all possible search spaces but in specific, ordered ones. Essentially, it works in a landscape in which each search step in the landscape informs upon the structure of the landscape. To translate this into a biological equivalent is that this particular search works, if the survival rate informs upon the fitness (i.e. offspring with variation and natural selection) . Of course, nature has much more upon her sleeves, but we shall leave it as that in order to keep things simple. However, another important aspect about evolution is that (again if we want to discuss it as a form of search) it is not a static search (Dembski mostly discusses static searches). The search is constantly changing by incorporating information about the current landscape. Thus you do not need to put the information into the algorithm beforehand, but let it learn by reading the landscape it walks over.

Well, the paper has been retracted now. Strong indication of lousy editorial work, though.

I have to add to that roughly half of the illegal immigrants present in the US do not cross the borders illegally, but have overstayed their Visa. An interesting question would be how many of these are parents. Another question is what problems these anchor babies bring and whether it would justify a new amendment.

Actually I am not that sure about the social pressure. For most of my colleagues I have no idea about their religious attitudes. The reason is that it simply does not factor in into science. I know a handful of Christians, mostly because they mentioned at one point or another that they are going to church (and are thus not available e.g. for meetings). It is likely that the vast majority are atheist, but it simply never came up.

Well technically there are more mechanisms out there. This is just the very first idea as described by Darwin.However, even in the absence of natural selection other events, as e.g. stochastic ones can influence the gene pool composition, depending on the size of the population, for instance.

Well the example that you put out for biomed scientists is a bit optimistic. Working at a national institute can give you 38k, but the average is lower. I have seen salaries from 30-40k. Of course it is not an automatic progression, you only make postdocs because you could not get a faculty or industrial position fast enough. Also note that faculty is not the end of the road. The really important bit is tenure, which is usually at least 5 years after the initial faculty position. Engineers enter faculty earlier. However it is expected that they enter earlier. I.e. if you do not find a faculty position within two postdocs at the latest, your chances of ever getting one will plummet. I have seen fresh PhDs immediately getting a position, but usually that only works if your advisor has good contacts and an interest in promoting your career.

However, tool use of wild animals has often been reported and is likely to have predated human tool use.

Well I am not sure how serious that is to be taken, however it was published in a peer reviewed journal (low impact, but still). Influenza or not influenza: Analysis of a case of high fever that happened 2000 years ago in Biblical time Kam LE Hon email, Pak C Ng email and Ting F Leung email Department of Paediatrics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China Virology Journal

Franklin's story actually gives important insights into the live in academia (and I believe most of it still holds true). One way to look at it was the fact that she did not provided enough balance between communication (including handwaving) and secrecy. It probably did not help that she was a woman. Regarding bad scientists, I would basically put people in that deliberately conducted fraud. This includes e.g. the famous autism fraud and ethical misbehavior conducted by Wakefield. Of course one could argue that they do not deserve to be called scientists.

From memory there are four bones involved in forming the knee join: femur, tibia, fibula and patella. The four bar linkage is simply established between femur and tibia with linkages by ligaments, though. At least, if I recall correctly. It has been a long, long while since I last worked with something that had knees....

Multicellularity arose several times (even in prokaryotes, to some extent) throughout history, if that was the question. Edit: cross-posted.

There are different definitions for synteny. Classically it was used to define genes on a given chromosome whose distance was unknown. More recently it has been used to actually describe genes co-localized in a genomic block. There are some finer points to it as well, that I will ignore for now. However, neither of these definitions describe the scenario in the OP. A single gene can, obviously not be co-localized in any way. What is being described is most likely an orthologous relationship, i.e. separation by speciation (in theory they could be also be paralogs, if duplication occurred first, but let us ignore that for now). In order to have any form of synteny (according to modern use) the scenario should be like this: Genes A and B are localized in a given genomic area in humans and in mouse we have an area containing two orthologous genes. They would then have a syntenic relationship. In other words, synteny is normally referred to conserved blocks, not single genes. Now, if the OP is slightly rephrased as e.g.: Gene A and B are within syntenic blocks, Not necessarily, as some definitions of synteny do not require the correct order or colinearity. Conversation can also be the existence of orthologous genes in any order. To summarize, if you deal with an old-school geneticist you probably should not use the term synteny to describe the relationship between species. If you look just as a single genes, use paralogous or orthologous instead. If looking at blocks and you use the modern definition you can use synteny, if you want to respect the historic term use conserved gene neighborhood instead, and apply the term collinearity when appropriate.

This thread started with speculations and did not improve. Thus a warm welcome to the speculations forum.

n+1

Not necessarily. If the required element is abundant there will no selective pressure to maintain them. I.e. mutations can occur within this genes without strong negative effects on the organism. There are scenarios, in which that may be an advantage as flows towards the synthesis of the abundant nutrients could be diverted to something that is more needed. However, synthesis pathways are normally strictly regulated anyway. One would have then to take into account the underlying regulatory networks and the potential effects of disruptions of those by mutations to estimate their impact. In many cases a neutral assumption comes close to what happens, though.

I wouldn't know a single analytical technique that requires some kind of interaction and is thus indirect. Not even our senses provide direct measurements (and we have to, one way or another plug the measurements into our senses, even if it is just via a screen). Despite the fact that it has indeed been observed species is a lousy hallmark of evolution. This is in fact the case because evolution happens and results in gradual changes within and between populations. However the species concept is something we plug on top of it for easy classifications purposes. It is only partially matched by nature. It is especially appalling when we go down to bacteria, for instance.

The article I was refering to was this one: Circulation. 2006 Jun 13;113(23):2690-6. Critical time window for intra-arrest cooling with cold saline flush in a dog model of cardiopulmonary resuscitation. Nozari A, Safar P, Stezoski SW, Wu X, Kostelnik S, Radovsky A, Tisherman S, Kochanek PM.

I think they basically used hypothermia to minimize brain damage. Key was to induce the hypothermia quickly after cardiac arrest. If that was delayed, most died. It is more a means to delay death rather than bringing back the dead. It depends a bit on the definition of course, but biologically rarely something happens immediate.

Also it would be an oversimplification to attribute everything to specific adaptations (i.e. exclusively in terms of selective advantages or disadvantages). Except in cases of extreme selective pressures other mechanisms are involved in governing the spread of a given trait.

Also I object against biologists being bunched together with medical sciences.

It depends on how broad you want to define the microbial composition. There are already differences between individual humans in terms of composition, for instance. At the same time the composition is dynamic and if we provide similar ecological niches, similar compositions are to be expected. Certain bacteria (as e.g. Escherichia) are found in many mammals as well as birds, whereas e.g. Bifidobacterium is mainly present in pigs and humans, also in the rumen of cows (but they get digested before they can become feces), but not in poultry, for instance.

One should note that up until recently the German system is completely different from the American one, not only medical school. In Germany you choose a subject (e.g. biology, physics, chemistry etc.) and the whole curriculum is created around these topics. I.e. biologists get a different chemistry training than chemists. Thus the medical school equivalent basically does the same as any other discipline. I disagree that highschools in Germany have advanced labwork, though. I do recall that calculus is part of the basic highschool curriculum, though.

It depends on the selective pressure the organism face to maintain a small genome size. Best example are viruses who only have a very small genome and face physical restrictions in size. Many bacteria also have a selective advantage (faster propagation) when it comes to having smaller size, though there is trade-off with metabolic versatility. More complex eukaryotes have less restriction and therefore are able to maintain larger genomes, even when they serve no immediate purpose. Note that the accumulated "junk" can gain functions at some point as they can serve as a base for genetic variability that organisms with small genomes do not possess. Also they can serve as harmless hot spots for viruses etc. At this point it may be useful to make it clearer what everybody is talking about. For instance whole genome size vs ORFs vs non-coding functional regions vs regions with unknown function. Or another example is what one means with expressed. E.g. under regulatory control or just dysfunctional in its expression (e.g. by mutation).

Getting no products is indeed often due to primers. You should check whether they are as "optimal" as possible (e.g. checking for repeat runs, unspecific binding, GC content etc.). While one could ascertain proper binding of individual primers to the template, most of the time it is easier and cheaper just to generate new primers. If the GC content is high you may want to use additives to lower melting temperature, for instance. I also assume that the buffer also includes the ions that the polymerase needs (usually Mg2+). If it is separate from the rest of the buffer you can also try changing that concentration.

Heh, I wouldn't be surprised if that this surfaced as an attempt to, say, renounce citizenship of a a recent US politician that got a Nobel price